Contacts of the helix formed by residues 656 - 661 (chain I) in PDB entry 6PSS
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 SER 656 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I ARG* 6.4 2.0 - - - -
19I PRO 5.2 3.1 - - - -
20I GLN* 3.5 30.0 + - - -
578I TYR* 2.7 36.0 + - - -
619I ALA* 3.7 14.2 - - - +
654I ASP* 3.5 1.9 - - - +
655I VAL* 1.3 79.4 - - - +
657I THR* 1.3 63.6 + - - +
658I GLN* 4.1 4.6 + - - -
659I GLN* 3.4 23.5 + - - +
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Residues in contact with THR 657 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I ARG* 5.0 11.0 - - + +
619I ALA* 3.8 20.2 - - + +
620I ASN* 4.2 15.0 - - + +
656I SER* 1.3 70.8 - - - +
658I GLN* 1.3 61.0 + - - +
659I GLN 3.1 6.5 + - - -
660I VAL* 4.2 4.9 + - - +
1187I PHE* 3.7 45.9 + - - +
1188I ASP* 3.5 27.4 + - - +
769J VAL* 3.9 25.6 - - + +
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Residues in contact with GLN 658 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I GLN* 4.9 11.4 + - - +
24I VAL* 5.1 3.5 - - - +
577I VAL* 4.1 7.7 - - + +
578I TYR* 4.1 23.7 + - + +
656I SER* 3.2 2.1 + - - +
657I THR* 1.3 78.1 + - - +
659I GLN* 1.3 60.2 + - - +
660I VAL 3.3 1.6 - - - -
661I VAL* 3.3 29.3 + - + +
666I SER* 4.2 6.5 + - - -
702I THR 4.3 11.3 + - - -
703I GLY 5.6 0.4 - - - -
704I MET* 3.3 39.4 - - - +
1185I PRO* 5.0 5.8 - - + +
1186I VAL* 3.5 37.7 - - + +
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Residues in contact with GLN 659 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555I TYR* 3.7 18.1 - - + -
556I GLY* 3.3 13.1 - - - +
576I SER* 2.9 19.6 + - - -
577I VAL* 5.0 0.2 - - - -
578I TYR* 3.5 29.3 + - + -
589I THR* 3.5 15.3 + - - +
590I PRO* 3.4 18.0 - - - +
591I TYR* 3.7 16.4 + - - -
654I ASP* 3.6 32.4 - - + +
655I VAL* 4.0 9.2 + - - +
656I SER* 3.4 17.7 + - - +
657I THR 3.1 3.2 - - - -
658I GLN* 1.3 76.9 - - - +
660I VAL* 1.3 62.9 + - - +
661I VAL 3.4 0.2 - - - -
769J VAL* 6.2 1.1 - - + -
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Residues in contact with VAL 660 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555I TYR* 4.1 24.9 - - + -
556I GLY 4.3 6.8 + - - +
558I VAL 4.0 3.5 - - - +
559I CYS* 4.0 3.1 - - - -
560I PRO* 3.2 21.4 - - + +
561I ILE* 5.8 0.7 - - + -
576I SER* 4.2 3.1 + - - -
657I THR 4.2 2.8 + - - +
658I GLN 3.3 0.2 - - - -
659I GLN* 1.3 80.6 - - - +
661I VAL* 1.3 77.5 + - + +
1187I PHE* 4.1 11.7 - - + -
769J VAL* 3.6 28.7 - - + +
772J TYR* 6.1 1.6 - - + -
773J PHE* 3.6 35.7 - - + +
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Residues in contact with VAL 661 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559I CYS* 3.6 6.7 - - - -
561I ILE* 3.7 29.6 - - + -
576I SER* 3.2 4.8 + - - -
577I VAL* 3.2 28.1 + - - +
658I GLN* 3.3 20.4 - - - +
660I VAL* 1.3 93.7 - - + +
662I SER* 1.3 69.0 + - - +
665I ALA* 4.3 7.0 - - + +
666I SER* 3.8 19.5 - - - -
671I LEU* 4.1 14.6 - - + -
1186I VAL* 4.3 9.6 - - + -
1187I PHE* 4.2 4.0 - - + -
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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