Contacts of the helix formed by residues 480 - 499 (chain C) in PDB entry 3SRF
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 ALA 480 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478C GLN* 3.3 3.9 - - + +
479C GLU* 1.3 77.5 - - - +
481C TRP* 1.3 65.4 + - - +
482C ALA* 3.4 2.0 - - + +
483C GLU* 3.3 26.1 + - + +
484C ASP* 3.1 21.3 + - - +
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Residues in contact with TRP 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C GLU* 4.5 13.0 - - - -
478C GLN 5.2 0.9 - - - -
479C GLU 3.6 4.7 + - - +
480C ALA* 1.3 69.5 - - - +
482C ALA* 1.3 57.0 + - - +
484C ASP* 3.1 14.2 + - + +
485C VAL* 2.8 54.5 + - + +
488C ARG* 3.4 30.3 - - - -
513C GLY* 3.3 30.1 + - - -
514C TRP 3.6 15.9 + - - -
515C ARG* 3.6 7.1 - - + +
516C PRO* 3.5 57.9 - - + -
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Residues in contact with ALA 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480C ALA* 3.4 2.1 - - + +
481C TRP* 1.3 80.1 - - - +
483C GLU* 1.3 69.8 + - + +
485C VAL* 3.8 5.6 - - - +
486C ASP* 2.9 37.4 + - - +
514G TRP* 6.6 0.2 - - + -
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Residues in contact with GLU 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478C GLN* 4.2 17.4 - - + +
480C ALA* 3.3 26.2 + - + +
481C TRP 3.2 0.8 - - - -
482C ALA* 1.3 86.8 - - - +
484C ASP* 1.3 60.8 + - - +
486C ASP* 3.7 7.8 - - - +
487C LEU* 2.9 31.4 + - - +
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Residues in contact with ASP 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454C ARG* 2.7 39.9 + - - -
477C VAL* 3.8 8.0 - - - +
478C GLN* 3.2 37.9 + - + +
480C ALA 3.1 13.1 + - - +
481C TRP* 3.1 20.9 + - + +
483C GLU* 1.3 76.5 - - - +
485C VAL* 1.3 61.5 + - - +
487C LEU* 3.5 2.7 + - - +
488C ARG* 3.0 46.7 + - - +
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Residues in contact with VAL 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C LEU* 3.5 9.0 - - + +
481C TRP* 2.8 50.7 + - + +
482C ALA* 3.8 6.5 - - - +
484C ASP* 1.3 72.9 - - - +
486C ASP* 1.3 68.1 + - - +
488C ARG* 3.5 17.7 - - - +
489C VAL* 3.1 29.9 + - + +
512C THR* 3.8 30.7 - - + +
513C GLY 4.3 5.8 - - - +
525C ARG* 4.4 9.4 - - - +
514G TRP* 5.7 4.3 - - + -
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Residues in contact with ASP 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482C ALA* 2.9 27.3 + - - +
483C GLU* 3.7 9.4 - - - +
484C ASP 3.4 0.2 - - - -
485C VAL* 1.3 79.2 - - - +
487C LEU* 1.3 55.8 + - - +
489C VAL* 3.1 7.3 + - - +
490C ASN* 2.8 49.1 + - - +
525C ARG* 5.0 5.4 + - - +
514G TRP* 4.6 15.5 + - - -
515G ARG* 5.3 6.8 + - - -
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Residues in contact with LEU 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454C ARG* 3.7 26.2 - - - +
473C CYS* 4.0 4.5 - - - -
475C ASP* 3.8 35.3 - - + +
476C PRO 4.7 0.9 - - - +
478C GLN* 3.8 27.8 - - - +
483C GLU 2.9 17.8 + - - +
484C ASP* 3.7 8.5 - - - +
486C ASP* 1.3 77.1 - - - +
488C ARG* 1.3 72.9 + - + +
490C ASN* 3.4 6.3 + - - +
491C PHE* 3.0 27.9 + - - +
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Residues in contact with ARG 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C LEU* 3.7 38.1 - - + +
431C THR 5.4 1.4 + - - +
432C GLU* 4.5 13.1 + - - +
452C VAL* 3.5 36.1 + - + +
453C THR* 6.1 0.2 - - - +
454C ARG* 3.5 30.8 - - - +
473C CYS* 4.2 5.8 - - + -
481C TRP* 3.4 32.1 - - - -
484C ASP* 3.0 34.3 + - - +
485C VAL* 3.5 21.8 - - - +
487C LEU* 1.3 92.6 - - + +
489C VAL* 1.3 62.0 + - - +
491C PHE* 3.3 19.2 - - - +
492C ALA 3.3 5.5 + - - -
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Residues in contact with VAL 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C ILE* 4.7 3.8 - - + -
430C LEU* 3.7 24.5 - - + -
485C VAL* 3.1 22.2 + - + +
486C ASP* 3.1 6.9 + - - +
488C ARG* 1.3 73.7 - - - +
490C ASN* 1.3 63.0 + - - +
492C ALA* 2.9 23.2 + - - +
493C MET* 3.0 28.5 + - + +
510C VAL* 3.7 35.7 - - + -
512C THR* 4.0 5.6 - - + -
525C ARG* 4.6 11.0 - - - +
527C VAL* 5.8 1.8 - - + -
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Residues in contact with ASN 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486C ASP* 2.8 36.2 + - - +
487C LEU* 3.8 5.7 - - - +
489C VAL* 1.3 74.3 - - - +
491C PHE* 1.3 56.4 + - - +
493C MET* 3.3 8.8 + - - +
494C ASN* 3.0 42.1 + - - +
530C PRO* 4.1 25.3 - - - +
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Residues in contact with PHE 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C PRO* 3.5 37.5 - - + -
102C ILE* 4.0 21.1 - - + -
452C VAL* 4.3 4.0 - - + -
471C VAL* 3.6 35.2 - - + -
472C LEU 3.8 14.4 - - - -
473C CYS* 3.7 37.7 - - + -
474C LYS 5.2 1.1 - - - -
475C ASP* 5.4 7.0 - - - +
487C LEU 3.0 13.8 + - - +
488C ARG* 3.3 13.5 - - - +
490C ASN* 1.3 76.5 - - - +
492C ALA* 1.3 56.4 + - - +
494C ASN* 3.2 9.0 + - - +
495C VAL* 2.9 35.2 + - + +
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Residues in contact with ALA 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C ILE* 3.6 21.8 - - + -
450C ILE* 3.7 16.8 - - + +
452C VAL* 3.3 28.7 - - + -
488C ARG 3.3 1.2 + - - -
489C VAL 2.9 10.8 + - - +
491C PHE* 1.3 79.8 - - - +
493C MET* 1.3 59.0 + - - +
495C VAL* 3.6 10.3 - - - +
496C GLY 3.1 21.0 + - - -
502C PHE* 3.6 8.8 - - - -
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Residues in contact with MET 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C ILE* 3.6 22.7 - - + -
489C VAL* 3.0 31.6 + - + +
490C ASN* 3.5 19.3 - - - +
491C PHE 3.2 0.4 - - - -
492C ALA* 1.3 76.8 - - - +
494C ASN* 1.3 66.8 + - - +
497C LYS* 3.3 19.3 + - - +
502C PHE* 3.3 39.3 - - + -
508C VAL* 3.8 13.9 - - + -
527C VAL* 5.2 4.5 - - - -
528C PRO 4.7 1.6 - - - +
529C VAL* 3.8 18.6 - - + -
530C PRO* 3.6 32.8 - - + -
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Residues in contact with ASN 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C ILE* 3.5 25.7 - - + +
490C ASN* 3.0 23.9 + - - +
491C PHE* 3.7 5.7 - - - +
493C MET* 1.3 78.4 - - - +
495C VAL* 1.3 66.1 + - - +
497C LYS* 4.1 17.3 + - - +
498C ALA* 3.3 22.0 + - - +
530C PRO* 6.1 0.5 - - - +
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Residues in contact with VAL 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C PRO 5.1 0.2 - - - +
102C ILE* 4.0 25.4 - - + +
450C ILE* 4.8 8.5 - - + -
469C PHE* 6.5 0.7 - - + -
471C VAL* 3.6 38.6 - - + -
491C PHE* 2.9 34.9 + - + +
492C ALA* 3.6 9.9 - - - +
494C ASN* 1.3 76.7 - - - +
496C GLY* 1.3 58.5 + - - +
498C ALA* 3.2 4.3 + - - +
499C ARG* 2.9 47.4 + - + +
501C PHE* 5.2 4.3 - - + -
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Residues in contact with GLY 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450C ILE* 4.4 0.7 - - - -
492C ALA 3.1 8.3 + - - -
493C MET 3.6 0.2 + - - -
494C ASN 3.4 0.2 - - - -
495C VAL* 1.3 79.5 - - - +
497C LYS* 1.3 58.6 + - - +
500C GLY 3.1 1.9 + - - -
501C PHE* 2.7 45.9 + - - -
502C PHE* 3.3 33.5 + - - -
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Residues in contact with LYS 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493C MET* 3.3 24.0 + - - +
494C ASN* 4.2 16.1 + - - +
495C VAL 3.3 0.2 - - - -
496C GLY* 1.3 74.6 - - - +
498C ALA* 1.3 63.3 + - - +
500C GLY* 3.2 13.0 + - - -
502C PHE* 3.3 24.8 - - + +
503C LYS* 4.7 2.9 - - - -
504C LYS* 4.9 9.5 - - + +
529C VAL* 3.8 15.0 - - + -
530C PRO* 2.9 31.8 + - - +
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Residues in contact with ALA 498 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C ILE* 3.7 18.2 - - + -
103C LEU* 4.3 18.4 - - + +
494C ASN 3.3 16.4 + - - +
495C VAL 3.2 4.6 + - - +
497C LYS* 1.3 81.1 - - - +
499C ARG* 1.3 60.5 + - - +
500C GLY 3.2 0.7 + - - -
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Residues in contact with ARG 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C THR* 3.9 13.7 + - - -
102C ILE 4.2 8.9 + - - -
103C LEU* 2.8 56.6 + - - +
104C TYR 4.9 0.6 + - - -
105C ARG* 2.8 50.6 - - - +
495C VAL* 2.9 40.2 + - + +
498C ALA* 1.3 75.9 - - - +
500C GLY* 1.3 59.9 + - - +
501C PHE* 3.3 35.6 + - + -
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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) + - + + + + + -
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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