Contacts of the helix formed by residues 3486 - 3507 (chain C) in PDB entry 2DQZ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER3486 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3451C TYR* 4.4 1.0 + - - -
3454C SER* 5.6 0.4 - - - -
3484C GLY 3.2 7.0 + - - -
3485C ALA* 1.3 75.0 - - - +
3487C GLU* 1.3 65.7 + - - +
3488C GLU* 3.4 14.8 + - - +
3489C GLU* 2.9 23.9 + - - +
3490C ILE* 2.8 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU3487 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3485C ALA 3.8 0.8 + - - -
3486C SER* 1.3 71.7 - - - +
3488C GLU* 1.3 52.3 + - - +
3490C ILE* 3.9 25.1 - - - +
3491C ARG* 2.7 70.9 + - - +
3494C LYS* 5.9 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU3488 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3451C TYR* 3.0 30.0 + - - -
3486C SER* 3.1 10.3 + - - +
3487C GLU* 1.3 79.3 - - - +
3489C GLU* 1.3 56.3 + - - +
3491C ARG* 3.5 17.4 + - - +
3492C LEU* 3.1 24.3 + - - +
3531C ALA* 3.2 31.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU3489 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3451C TYR* 3.3 31.2 + - + +
3453C PRO* 3.2 10.4 - - - +
3454C SER* 2.8 46.7 + - - -
3455C PHE* 3.2 21.3 - - + -
3473C PHE* 5.4 0.3 - - - +
3474C SER* 5.3 3.0 + - - +
3479C PRO* 4.0 6.9 - - + +
3485C ALA* 3.3 17.9 - - + +
3486C SER* 2.9 15.8 + - - +
3488C GLU* 1.3 76.2 - - - +
3490C ILE* 1.3 66.3 + - - +
3491C ARG 3.1 0.2 - - - -
3492C LEU* 3.2 5.3 + - + +
3493C SER* 3.0 23.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE3490 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3479C PRO* 3.9 17.3 - - + +
3480C PHE* 3.5 30.9 - - + -
3485C ALA* 3.3 32.5 - - + +
3486C SER 2.8 14.6 + - - +
3487C GLU* 3.4 31.4 - - - +
3489C GLU* 1.3 75.6 - - - +
3491C ARG* 1.3 62.8 + - - +
3493C SER* 3.4 3.8 + - - -
3494C LYS* 3.2 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG3491 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3487C GLU* 2.7 51.2 + - - +
3488C GLU* 3.5 21.0 - - - +
3489C GLU 3.1 0.2 - - - -
3490C ILE* 1.3 74.7 - - - +
3492C LEU* 1.3 65.5 + - - +
3494C LYS* 3.1 11.8 + - + +
3495C MET* 3.1 23.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3492 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3449C PHE* 4.1 4.7 - - + -
3451C TYR* 3.5 50.7 - - + -
3474C SER* 3.7 18.2 - - - +
3488C GLU 3.1 14.5 + - - +
3489C GLU* 3.5 9.6 - - + +
3491C ARG* 1.3 76.6 - - - +
3493C SER* 1.3 63.5 + - - +
3495C MET* 3.4 27.6 + - + +
3496C VAL* 3.0 28.2 + - + +
3529C ILE* 3.8 7.6 - - + -
3530C GLY* 3.2 33.9 - - - +
3531C ALA* 6.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER3493 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3474C SER* 2.8 35.2 + - - -
3477C GLY* 3.2 21.1 - - - -
3479C PRO* 3.8 17.7 - - - -
3480C PHE* 4.1 4.7 - - - -
3489C GLU 3.0 12.5 + - - -
3490C ILE 3.6 8.3 - - - -
3491C ARG 3.2 0.4 - - - -
3492C LEU* 1.3 77.9 - - - +
3494C LYS* 1.3 62.7 + - - +
3496C VAL* 3.2 2.8 + - - +
3497C MET* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS3494 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3160C HIS* 4.4 15.0 - - - +
3161C GLU* 4.1 2.5 - - - +
3480C PHE* 3.5 34.3 - - + -
3487C GLU* 5.9 2.8 + - - +
3490C ILE* 3.2 13.1 + - + +
3491C ARG* 3.1 14.2 + - - +
3493C SER* 1.3 77.9 - - - +
3495C MET* 1.3 61.1 + - - +
3497C MET* 3.6 9.2 + - - +
3498C LYS* 3.1 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET3495 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3491C ARG* 3.1 11.1 + - + +
3492C LEU* 3.5 33.7 - - + +
3494C LYS* 1.3 79.3 - - - +
3496C VAL* 1.3 64.3 + - + +
3498C LYS* 3.0 13.0 + - - +
3499C PHE* 3.0 35.3 + - + -
3514C LEU* 3.7 21.8 - - + -
3515C PRO* 4.0 21.8 - - - -
3529C ILE* 4.4 7.6 - - + -
3530C GLY 4.4 0.9 - - - +
3533C THR* 3.1 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL3496 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3449C PHE* 4.7 2.5 - - + -
3471C GLU* 6.3 0.4 - - + -
3474C SER* 3.5 20.6 - - - +
3475C VAL* 3.8 36.3 - - + +
3492C LEU* 3.0 19.3 + - + +
3493C SER 3.5 5.8 - - - +
3495C MET* 1.3 78.6 - - + +
3497C MET* 1.3 65.0 + - - +
3498C LYS 3.1 0.3 + - - -
3499C PHE* 3.3 7.1 + - - -
3500C TRP* 3.1 40.9 + - + +
3529C ILE* 4.2 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET3497 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3156C ALA 4.4 0.9 - - - -
3157C LEU* 3.9 33.6 - - + +
3160C HIS* 4.0 20.0 - - + +
3161C GLU* 3.4 15.9 - - + +
3474C SER 3.4 8.3 - - - +
3475C VAL 3.4 18.8 - - - +
3477C GLY* 3.7 17.7 - - - -
3480C PHE* 3.6 35.9 - - + -
3493C SER* 2.9 23.2 + - - +
3494C LYS* 4.1 7.2 - - - +
3496C VAL* 1.3 72.9 - - - +
3498C LYS* 1.3 62.2 + - - +
3500C TRP* 3.6 6.6 - - - +
3501C ALA* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS3498 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3160C HIS 5.1 3.2 + - - -
3161C GLU* 3.3 33.0 + - - +
3494C LYS* 3.1 15.9 + - - +
3495C MET 3.0 10.4 + - - +
3497C MET* 1.3 75.6 - - - +
3499C PHE* 1.3 69.4 + - - +
3500C TRP 3.0 0.3 + - - -
3501C ALA* 3.6 0.7 - - - +
3502C ASN* 2.7 39.2 + - - +
3505C ARG* 4.8 0.4 - - - +
3512C GLU 5.7 3.8 - - - -
3514C LEU* 3.4 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE3499 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3347C MET* 5.2 0.2 - - - -
3495C MET* 3.0 42.8 + - + -
3496C VAL* 3.6 9.4 - - - +
3498C LYS* 1.3 78.9 - - - +
3500C TRP* 1.3 61.1 + - + +
3502C ASN 3.3 0.3 + - - -
3503C PHE* 2.8 35.2 + - - +
3509C PRO* 3.4 36.6 - - + +
3510C ASN* 4.9 2.0 - - - -
3514C LEU* 3.8 14.8 - - + -
3515C PRO* 3.6 38.8 - - + -
3517C TRP* 3.8 25.8 - + + -
3527C LEU* 3.6 24.2 - - + -
3529C ILE* 5.0 7.0 - - + -
3533C THR* 4.6 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP3500 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3136C MET* 4.2 14.0 - - + +
3157C LEU* 5.3 4.0 - - + -
3218C PHE* 4.1 11.4 - + - -
3244C ILE* 3.8 25.1 - - + +
3246C GLU* 3.0 30.6 + - + -
3347C MET* 4.0 15.7 - - - -
3447C TYR* 3.5 39.5 - + - -
3471C GLU* 5.5 1.6 - - + -
3475C VAL* 3.7 31.7 - - + +
3496C VAL* 3.1 31.7 + - + +
3497C MET* 3.6 11.0 - - - +
3499C PHE* 1.3 82.7 - - + +
3501C ALA* 1.3 51.7 + - - +
3503C PHE* 2.8 12.0 + - - +
3504C ALA* 2.7 32.6 + - - +
3517C TRP* 4.2 15.7 - + - -
3529C ILE* 4.2 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3501 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3136C MET* 4.4 7.1 - - - +
3157C LEU* 5.2 1.1 - - + -
3161C GLU* 3.3 29.6 - - + +
3163C VAL* 4.4 6.2 - - + +
3497C MET 2.9 10.9 + - - +
3498C LYS 3.7 0.2 - - - +
3500C TRP* 1.3 75.6 - - - +
3502C ASN* 1.3 56.2 + - - +
3504C ALA* 3.1 10.3 + - - +
3505C ARG* 2.7 58.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN3502 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3498C LYS* 2.7 28.0 + - - +
3499C PHE 3.5 0.2 - - - +
3501C ALA* 1.3 71.8 - - - +
3503C PHE* 1.3 53.7 + - - +
3505C ARG* 3.1 27.9 + - - +
3506C ASN* 2.8 38.4 + - - +
3508C ASN 3.0 10.8 - - - +
3509C PRO 3.0 28.7 + - - +
3510C ASN 3.8 11.1 + - - +
3511C GLY* 3.9 7.0 - - - -
3514C LEU* 3.5 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE3503 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3216C THR* 4.8 0.9 - - + -
3242C ARG* 3.1 20.9 - - + -
3243C ALA 3.3 21.1 - - - -
3244C ILE* 3.7 25.4 - - + -
3345C PRO* 3.6 32.8 - - + -
3346C TYR 3.8 2.2 - - - -
3347C MET* 3.6 27.4 - - + -
3445C TYR* 4.0 16.6 - + - -
3499C PHE 2.8 14.4 + - - +
3500C TRP* 3.1 8.3 - - - +
3502C ASN* 1.3 77.4 - - - +
3504C ALA* 1.3 58.8 - - - +
3507C GLY* 2.5 56.9 + - - -
3508C ASN* 3.3 12.3 + - - -
3509C PRO* 4.0 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3504 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3134C PRO* 4.5 15.3 - - + +
3136C MET* 4.0 28.9 - - + -
3214C SER* 3.8 9.0 + - - -
3216C THR* 3.5 22.9 + - - +
3242C ARG* 2.6 26.5 + - - -
3500C TRP 2.7 15.2 + - - +
3501C ALA* 3.3 10.5 - - - +
3503C PHE* 1.3 75.7 - - - +
3505C ARG* 1.3 56.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG3505 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3134C PRO* 4.1 22.5 - - + +
3161C GLU* 3.0 48.1 + - - -
3162C ASN 4.6 1.6 + - - -
3163C VAL* 4.0 7.3 - - - +
3214C SER* 4.7 3.4 + - - -
3242C ARG* 3.7 10.4 + - - -
3498C LYS* 4.8 1.2 - - - +
3501C ALA* 2.7 33.0 + - - +
3502C ASN* 3.1 30.2 + - - +
3504C ALA* 1.3 77.2 - - - +
3506C ASN* 1.3 74.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN3506 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3242C ARG* 4.2 8.7 + - - +
3502C ASN* 2.8 24.9 + - - +
3505C ARG* 1.3 91.5 - - - +
3507C GLY* 1.3 64.1 + - - +
3508C ASN* 4.0 17.4 + - + +
3510C ASN 4.8 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY3507 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3242C ARG* 3.6 17.0 - - - +
3345C PRO* 3.9 26.2 - - - +
3443C PRO* 4.8 3.6 - - - +
3445C TYR* 3.8 10.4 + - - -
3503C PHE* 2.5 41.8 + - - -
3506C ASN* 1.3 73.2 - - - +
3508C ASN* 1.3 57.1 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il