Contacts of the helix formed by residues 429 - 447 (chain C) in PDB entry 3GZN
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 GLU 429 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C ASP 3.7 3.3 + - - +
428C ASN* 1.3 76.6 + - - +
430C ILE* 1.3 63.3 + - - +
431C VAL 3.2 0.2 - - - -
432C LEU* 2.9 32.2 + - + +
433C TYR 3.7 1.7 + - - -
528C ILE* 3.8 33.2 - - + +
530C SER* 4.7 8.5 - - - -
535C THR* 2.6 42.4 + - - +
536C SER* 3.5 3.4 + - - +
537C ALA* 3.9 29.5 - - + +
539C PHE* 3.9 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 430 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C ILE* 4.3 24.5 - - + +
422C SER* 3.8 10.3 - - - -
423C MET* 3.5 32.1 - - + +
428C ASN* 2.7 26.5 + - - +
429C GLU* 1.3 74.2 - - - +
431C VAL* 1.3 63.6 + - - +
433C TYR* 3.0 30.1 + - + +
434C LEU* 2.9 20.1 + - + +
526C THR* 6.2 0.2 - - + -
528C ILE* 5.6 0.4 - - + -
539C PHE* 3.7 34.6 - - + -
541C LEU* 4.3 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 431 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C MET* 3.7 27.6 - - + -
426C PRO 3.7 18.6 - - - +
427C ASP 4.2 0.4 - - - -
428C ASN 2.8 27.6 + - - +
430C ILE* 1.3 75.8 - - - +
432C LEU* 1.3 56.4 + - + +
434C LEU* 2.9 10.0 + - + +
435C MET* 2.7 37.6 + - - +
481C VAL* 3.8 28.7 - - + -
485C TYR* 4.0 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 432 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C VAL* 3.9 29.4 - - + -
429C GLU* 2.9 22.3 + - - +
431C VAL* 1.3 79.0 - - + +
433C TYR* 1.3 56.2 + - - +
435C MET* 3.6 1.9 + - - +
436C LEU* 3.0 33.8 + - - +
485C TYR* 3.8 33.0 - - + -
489C PHE* 3.9 19.2 - - + -
528C ILE* 3.9 13.2 - - + -
530C SER* 3.5 35.7 - - - +
532C MET* 5.5 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 433 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C TYR* 3.6 31.6 - + - -
408C GLU* 2.6 37.2 + - - +
409C TYR* 4.3 2.3 - - - -
419C ILE* 5.0 10.5 - - + -
429C GLU 3.7 2.0 + - - -
430C ILE* 3.0 29.5 + - + +
432C LEU* 1.3 77.3 - - - +
434C LEU* 1.3 78.4 + - + +
436C LEU* 3.1 12.8 + - + +
437C ARG* 3.0 61.3 + - + +
471C PHE* 4.9 2.5 - + - -
526C THR* 4.4 2.5 - - + -
528C ILE* 3.9 14.2 - - + +
541C LEU* 3.5 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 434 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C ILE* 4.1 20.4 - - + -
423C MET* 3.8 36.6 - - + -
430C ILE* 2.9 16.5 + - + +
431C VAL* 2.9 9.3 + - - +
433C TYR* 1.3 87.2 - - + +
435C MET* 1.3 58.4 + - + +
437C ARG* 3.2 5.2 + - - +
438C ALA* 2.9 26.7 + - - +
468C LEU* 4.2 10.9 - - + +
471C PHE* 3.5 34.2 - - + -
472C LEU* 4.2 8.1 - - + -
477C LEU* 4.7 2.0 - - + -
479C VAL* 4.4 11.9 - - + -
481C VAL* 4.5 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 435 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C VAL 2.7 19.5 + - - +
434C LEU* 1.3 73.8 - - + +
436C LEU* 1.3 59.0 + - - +
438C ALA* 3.1 6.8 + - + +
439C VAL* 2.8 33.1 + - + +
464C LEU* 3.8 23.6 - - + -
468C LEU* 4.0 27.1 - - + -
481C VAL* 4.3 5.8 - - + -
485C TYR* 4.0 18.6 - - + -
486C VAL* 3.7 33.2 - - + +
489C PHE* 3.5 44.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 436 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C ARG* 3.5 35.0 - - + +
163C TYR* 4.2 27.1 - - + -
166C VAL* 3.9 15.5 - - + -
168C TYR* 3.8 37.9 - - + -
432C LEU 3.0 24.2 + - - +
433C TYR* 3.1 11.4 + - + +
435C MET* 1.3 75.9 - - - +
437C ARG* 1.3 58.2 + - + +
439C VAL* 3.2 8.6 + - + +
440C ASP* 2.9 34.8 + - - +
489C PHE* 4.2 8.0 - - + -
528C ILE* 5.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 437 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C GLU* 4.4 11.0 + - - +
408C GLU 4.3 4.0 + - - -
409C TYR* 3.2 61.1 + - - +
414C ILE* 5.7 2.6 - - - +
433C TYR* 3.0 51.4 + - + +
434C LEU 3.2 7.2 + - - +
436C LEU* 1.3 76.1 - - + +
438C ALA* 1.3 63.1 + - - +
440C ASP* 3.3 8.4 + - - +
441C ARG* 3.1 22.7 + - - +
471C PHE* 3.2 35.6 - - + -
475C TYR* 3.2 33.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 438 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434C LEU 2.9 13.3 + - - +
435C MET* 3.1 13.2 + - + +
437C ARG* 1.3 76.2 - - - +
439C VAL* 1.3 52.4 + - - +
441C ARG* 3.2 8.9 + - - +
442C PHE* 2.8 33.3 + - - +
464C LEU* 4.1 11.4 - - + -
467C CYS* 3.8 6.5 - - - +
468C LEU* 3.7 40.6 - - + +
471C PHE* 4.7 4.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 439 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C ARG* 4.6 1.8 - - - +
163C TYR* 3.6 39.0 - - + +
435C MET* 2.8 20.7 + - + +
436C LEU* 3.5 7.0 - - - +
438C ALA* 1.3 73.6 - - - +
440C ASP* 1.3 61.9 + - - +
442C PHE* 3.2 3.8 + - - +
443C HIS* 2.8 27.4 + - - +
449C TYR* 3.7 19.0 - - + -
450C PRO* 4.1 6.3 - - + -
464C LEU* 3.9 23.3 - - + +
489C PHE* 4.0 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 440 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C LEU 5.4 0.2 - - - +
139C PRO* 5.3 0.7 - - - +
140C GLU* 3.3 48.5 + - + +
161C ARG* 2.6 43.5 + - - -
409C TYR* 4.4 7.3 + - - -
436C LEU* 2.9 16.8 + - - +
437C ARG* 3.6 4.9 - - - +
439C VAL* 1.3 73.6 - - - +
441C ARG* 1.3 64.7 + - - +
443C HIS* 3.4 7.3 + - - +
444C LYS* 3.2 24.8 + - - +
449C TYR* 4.4 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 441 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C GLU* 4.7 4.4 + - - +
437C ARG 3.1 13.0 + - - +
438C ALA 3.3 8.5 - - - +
440C ASP* 1.3 73.4 - - - +
442C PHE* 1.3 65.1 + - - +
444C LYS* 3.4 13.9 + - + +
445C GLN* 3.1 41.8 + - + +
467C CYS* 3.1 32.7 + - - +
470C GLY* 3.5 24.3 + - - -
471C PHE* 3.7 19.0 - - + +
474C GLU* 3.1 29.9 + - - +
475C TYR* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 442 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438C ALA 2.8 17.3 + - - +
439C VAL* 3.2 9.0 - - - +
441C ARG* 1.3 73.9 - - - +
443C HIS* 1.3 62.5 + - - +
445C GLN* 3.2 0.7 + - - +
446C GLN* 2.9 42.8 + - + +
448C ARG* 3.3 29.8 - - + -
449C TYR 3.6 3.6 - - - -
450C PRO* 3.5 36.8 - - + -
460C ASP* 4.0 17.5 - - - -
463C LYS* 3.7 31.2 - - + -
464C LEU* 3.9 32.8 - - + -
467C CYS* 3.6 14.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 443 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A SER* 5.5 3.8 - - - -
139C PRO* 4.6 20.0 - - + +
140C GLU 6.0 0.4 - - - -
439C VAL 2.8 19.2 + - - +
440C ASP* 3.6 7.2 - - - +
441C ARG 3.2 0.4 - - - -
442C PHE* 1.3 74.4 - - - +
444C LYS* 1.3 62.3 + - + +
447C GLY* 2.7 41.1 + - - -
448C ARG* 3.3 35.5 - - - +
449C TYR* 3.4 45.3 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 444 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C GLU* 4.5 23.4 + - + +
141C SER* 5.6 14.4 - - - +
440C ASP 3.2 11.3 + - - +
441C ARG* 3.7 14.8 - - + +
443C HIS* 1.3 83.2 - - + +
445C GLN* 1.3 68.2 + - + +
447C GLY* 4.4 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 445 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C ARG* 3.1 31.4 + - + +
442C PHE 3.5 8.5 - - - +
444C LYS* 1.3 82.3 - - + +
446C GLN* 1.3 76.7 + - + +
447C GLY 3.6 0.4 + - - -
467C CYS* 3.4 30.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 446 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A PRO* 5.9 0.9 - - - +
152A ASN* 4.8 11.3 + - - +
153A SER* 5.6 0.3 + - - -
442C PHE* 2.9 50.8 + - + +
445C GLN* 1.3 94.8 + - + +
447C GLY* 1.3 63.8 + - - +
448C ARG* 3.2 25.0 + - + +
463C LYS* 4.0 33.4 + - - +
467C CYS* 6.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 447 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A PRO* 4.2 17.3 - - - +
125A SER* 3.5 21.7 + - - -
443C HIS* 2.7 30.0 + - - -
444C LYS* 4.4 2.5 + - - -
445C GLN 3.6 1.8 + - - -
446C GLN* 1.3 72.8 - - - +
448C ARG* 1.3 56.6 + - - +
----------------------------------------------------------
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