Contacts of the helix formed by residues 495 - 504 (chain S) in PDB entry 5L4K
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 ARG 495 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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491S VAL* 3.0 17.3 + - + +
492S LYS* 3.3 40.8 - - - +
493S ALA 2.9 1.6 - - - -
494S MET* 1.3 81.2 - - + +
496S PHE* 1.3 65.1 + - + +
498S PRO* 3.3 14.5 - - - +
499S LYS* 3.5 12.5 + - - +
349T ILE 4.5 3.2 + - - -
350T VAL* 3.3 48.5 + - - +
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Residues in contact with PHE 496 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492S LYS 4.6 9.9 - - - -
493S ALA* 3.4 18.3 + - + +
494S MET 2.9 1.0 + - - -
495S ARG* 1.3 80.5 - - + +
497S PRO* 1.3 72.2 - - + +
499S LYS* 2.8 36.9 + - + +
500S SER* 3.1 8.1 + - - -
279U LYS* 5.8 1.1 - - - +
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Residues in contact with PRO 497 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493S ALA 3.9 4.0 - - - +
494S MET* 3.1 14.1 - - - +
496S PHE* 1.3 95.9 - - + +
498S PRO* 1.3 66.4 - - + +
499S LYS 3.1 0.2 + - - -
500S SER* 2.9 19.4 + - - -
501S TYR* 3.2 16.9 - - - +
278U ASN* 3.6 37.5 - - + +
279U LYS* 4.1 27.6 - - + +
282U ASN* 4.0 16.6 - - + +
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Residues in contact with PRO 498 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494S MET* 2.8 44.9 - - - +
495S ARG* 3.3 10.5 - - - +
497S PRO* 1.3 83.5 - - + +
499S LYS* 1.3 56.0 + - - +
501S TYR* 3.2 16.7 + - + +
502S ASN* 2.9 37.9 + - - +
278U ASN* 3.7 9.4 - - - +
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Residues in contact with LYS 499 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495S ARG 3.5 10.8 + - - +
496S PHE* 2.8 34.5 + - + +
498S PRO* 1.3 71.0 - - - +
500S SER* 1.3 66.6 + - - +
502S ASN* 3.3 12.0 + - + +
503S LYS* 2.9 44.7 + - - +
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Residues in contact with SER 500 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496S PHE 3.1 8.6 + - - -
497S PRO 2.9 15.6 + - - -
499S LYS* 1.3 80.3 - - - +
501S TYR* 1.3 69.3 + - - +
503S LYS* 3.1 24.6 - - - +
504S ASP* 3.4 5.5 + - - +
282U ASN* 3.1 21.4 + - - -
285U ALA* 5.7 0.5 - - - +
289U GLU* 4.8 17.3 - - - +
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Residues in contact with TYR 501 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497S PRO* 3.2 22.8 - - - +
498S PRO* 3.5 13.5 - - + +
499S LYS 3.2 0.6 - - - -
500S SER* 1.3 85.0 - - - +
502S ASN* 1.3 53.3 + - - +
503S LYS 3.1 1.1 - - - -
504S ASP* 2.6 44.9 + - + +
506S GLU* 3.8 11.7 - - - +
278U ASN* 3.5 15.7 + - - -
281U ALA* 3.1 17.5 - - + +
282U ASN* 3.0 31.6 + - - +
285U ALA* 3.9 25.4 - - + -
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Residues in contact with ASN 502 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498S PRO* 2.9 32.7 + - - +
499S LYS* 3.3 14.2 + - + +
501S TYR* 1.3 75.4 - - - +
503S LYS* 1.3 59.1 + - - +
504S ASP 2.8 14.5 - - - +
505S LEU* 4.9 0.5 - - - -
506S GLU* 2.6 35.6 + - - +
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Residues in contact with LYS 503 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499S LYS* 2.9 31.7 + - - +
500S SER* 3.1 16.6 - - - +
501S TYR 3.1 0.2 - - - -
502S ASN* 1.3 75.7 - - - +
504S ASP* 1.3 56.7 + - - +
505S LEU* 3.9 3.1 + - - +
289U GLU* 5.5 6.5 - - - +
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Residues in contact with ASP 504 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500S SER 3.4 3.2 + - - +
501S TYR* 2.6 37.4 + - - +
502S ASN 2.8 10.9 - - - +
503S LYS* 1.3 75.7 - - - +
505S LEU* 1.3 85.3 + - - +
506S GLU* 3.3 4.2 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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