Contacts of the strand formed by residues 85 - 89 (chain P) in PDB entry 4R2G
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 ASP 85 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5P TYR* 4.4 2.9 + - - -
6P VAL* 5.9 0.2 - - - -
36P TYR 3.9 0.7 - - - +
37P GLN* 3.7 2.3 - - - -
38P HIS* 2.9 41.8 + - + +
40P PRO* 4.0 16.1 - - - +
84P ALA* 1.3 74.9 - - - +
86P TYR* 1.3 61.2 + - - +
87P TYR* 4.0 17.8 + - + -
101P ALA* 3.7 19.9 - - + +
102P THR 3.2 4.9 - - - +
103P ARG* 2.6 49.9 + - - +
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Residues in contact with TYR 86 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21P ILE* 3.9 19.9 - - + +
35P TRP* 4.8 10.4 - - + -
36P TYR 3.6 2.2 - - - -
37P GLN* 3.1 28.5 + - + -
47P LEU* 3.4 33.7 - - + -
62P PHE* 4.0 2.3 - + - -
73P LEU* 3.7 11.2 - - + -
75P ILE* 3.5 25.7 - - + +
82P ASP* 2.8 34.7 + - - +
84P ALA* 3.6 19.5 - - + -
85P ASP* 1.3 74.4 - - - +
87P TYR* 1.3 63.3 + - - +
88P CYS 4.2 0.5 + - - -
100P GLY 4.0 1.4 - - - +
101P ALA* 3.3 3.3 - - - -
102P THR* 2.7 43.8 + - - +
104P LEU* 3.8 13.9 - - + -
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Residues in contact with TYR 87 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5P TYR* 4.0 6.8 + + - -
34P GLN 3.8 0.3 - - - +
35P TRP* 3.2 11.0 - - - -
36P TYR* 2.9 50.9 + - + +
38P HIS* 4.1 14.2 + - + -
85P ASP* 4.0 20.9 + - + -
86P TYR* 1.3 74.8 - - - +
88P CYS* 1.3 61.7 + - - +
89P HIS 4.0 0.7 - - - -
98P PHE* 4.1 19.1 - - + -
99P GLY 3.3 26.2 - - - -
100P GLY 4.1 2.2 - - - -
101P ALA* 3.0 29.5 - - + +
39Q GLN* 5.7 0.7 - - - +
44Q GLY* 3.7 10.4 - - - -
45Q LEU* 3.5 55.7 + - + +
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Residues in contact with CYS 88 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23P CYS* 2.1 54.6 - - + -
24P GLY 5.0 1.6 - - - +
25P ARG* 3.1 9.7 + - - -
33P VAL* 3.4 25.1 - - - -
34P GLN 3.3 4.7 - - - -
35P TRP* 3.4 24.2 - - + -
86P TYR 4.2 0.4 + - - -
87P TYR* 1.3 72.3 - - - +
89P HIS* 1.3 58.9 + - - +
90P MET 4.5 1.6 - - - -
98P PHE 2.8 19.5 + - - +
100P GLY 4.8 4.2 + - - +
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Residues in contact with HIS 89 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25P ARG* 3.7 0.9 - - - +
33P VAL* 3.7 1.2 - - - -
34P GLN* 2.7 35.6 + - + +
36P TYR* 3.9 30.2 + - + -
87P TYR 4.0 0.8 - - - -
88P CYS* 1.3 71.3 - - - +
90P MET* 1.3 60.2 + - - +
91P TRP* 3.0 47.5 + + - -
95P SER* 3.8 16.6 - + - -
97P SER 3.4 25.8 + - - -
98P PHE* 3.8 23.4 - + + -
47Q TRP* 3.6 21.0 - + - -
100Q TYR* 4.2 8.0 - - + +
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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