Contacts of the strand formed by residues 621 - 625 (chain C) in PDB entry 4P3N
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 VAL 621 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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614C PHE* 4.9 0.7 - - + -
619C ARG 3.8 0.8 - - - -
620C GLN* 1.3 88.9 - - + +
622C MET* 1.3 64.5 + - - +
623C VAL* 3.8 24.0 - - + -
641C PHE* 4.1 22.7 - - + -
646C PHE* 4.8 6.1 - - + -
647C MET 3.0 3.6 + - - +
648C ALA* 3.5 18.8 - - + -
649C ASP 2.9 24.4 + - - -
670C TYR* 3.3 12.0 - - - -
672C PHE* 3.3 8.5 - - + -
674C LEU* 3.9 19.5 - - + -
708C LEU* 4.2 16.8 - - + -
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Residues in contact with MET 622 (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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621C VAL* 1.3 72.3 - - - +
623C VAL* 1.3 67.8 + - - +
624C VAL* 3.7 4.8 + - + -
649C ASP* 3.9 10.1 - - + -
650C ILE 3.6 39.5 - - - +
651C ASP* 3.7 20.2 - - + +
665C ALA* 3.8 23.6 - - + -
670C TYR* 3.7 38.1 - - + +
672C PHE 2.9 11.3 + - - +
673C ILE* 3.3 9.0 - - + +
674C LEU 2.9 26.0 + - - +
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Residues in contact with VAL 623 (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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621C VAL* 3.8 17.0 - - + -
622C MET* 1.3 74.0 - - - +
624C VAL* 1.3 61.8 + - - +
625C PRO* 3.9 0.6 - - - +
634C ALA* 3.9 29.6 - - + +
637C VAL* 4.1 18.2 - - + -
638C ARG* 3.7 26.0 - - + +
641C PHE* 5.8 0.2 - - + -
649C ASP 2.9 19.3 + - - +
650C ILE* 3.2 15.1 - - + +
651C ASP 3.0 26.0 + - - -
674C LEU* 3.5 13.5 - - + +
676C VAL* 4.6 6.5 - - + -
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Residues in contact with VAL 624 (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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622C MET* 4.5 14.6 - - + +
623C VAL* 1.3 77.7 - - - +
625C PRO* 1.3 75.5 - - + +
651C ASP* 4.2 11.2 - - + -
658C LEU* 3.8 22.0 - - + -
661C LYS* 3.7 44.9 - - + +
662C ILE* 5.0 1.6 - - + +
665C ALA* 5.6 0.4 - - + -
673C ILE* 4.5 13.7 - - + -
674C LEU 2.9 10.7 + - - +
675C VAL* 3.3 8.3 - - + +
676C VAL* 2.9 26.0 + - - -
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Residues in contact with PRO 625 (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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623C VAL 3.9 5.2 - - - +
624C VAL* 1.3 96.4 - - + +
626C VAL* 1.3 63.0 - - - +
627C GLY 3.9 11.7 - - - +
630C CYS* 3.8 23.1 - - + +
631C ASP* 3.7 17.7 - - - +
634C ALA* 4.0 7.1 - - + -
651C ASP 3.2 22.4 - - - +
652C LEU* 3.9 12.6 - - + -
658C LEU* 4.8 2.1 - - - +
661C LYS* 4.7 9.0 + - - +
676C VAL* 3.3 10.8 - - + +
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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