Contacts of the strand formed by residues 34 - 38 (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 GLN 34 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32P ALA 3.8 11.2 + - - -
33P VAL* 1.3 81.0 + - - +
35P TRP* 1.3 62.8 + - - +
36P TYR* 3.7 23.3 - - + +
46P LEU* 4.1 2.2 - - + -
48P ILE 3.2 9.0 - - - +
49P TYR* 3.2 6.9 - - + -
50P ASN* 2.8 37.9 + - - +
87P TYR 3.8 0.5 - - - +
88P CYS* 3.3 4.0 - - - -
89P HIS* 2.7 44.6 + - + +
91P TRP* 4.1 9.5 - - - -
100Q TYR* 3.2 60.1 - - + +
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Residues in contact with TRP 35 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21P ILE* 3.4 37.9 - - + -
23P CYS* 3.7 18.4 - - + -
33P VAL* 3.6 18.4 - - + +
34P GLN* 1.3 71.4 - - - +
36P TYR* 1.3 56.3 + - - +
46P LEU* 3.8 2.3 - - - +
47P LEU* 2.8 36.0 + - + +
48P ILE* 2.9 44.7 + - + +
51P ASN 5.0 1.7 + - - -
64P GLY* 4.8 5.7 - - - -
65P THR 5.5 0.8 - - - +
71P ALA* 4.3 1.0 - - - +
72P THR* 3.9 8.5 + - - +
73P LEU* 3.2 48.9 - - + +
86P TYR* 4.8 7.6 - + + -
87P TYR 3.2 22.4 - - - -
88P CYS* 3.4 35.0 - - + -
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Residues in contact with TYR 36 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34P GLN* 3.7 19.8 - - + +
35P TRP* 1.3 74.5 - - - +
37P GLN* 1.3 61.9 + - - +
44P PRO* 4.8 8.3 - - + -
45P ILE 3.3 7.0 - - - +
46P LEU* 3.5 36.3 - - + -
47P LEU* 4.1 3.1 - - - -
85P ASP 3.9 0.2 - - - +
86P TYR* 3.6 4.9 - - - +
87P TYR* 2.9 47.9 + - + +
89P HIS* 3.9 19.3 + - + -
98P PHE* 4.1 24.7 - + - -
45Q LEU* 5.3 2.5 - - + -
100Q MET* 3.2 55.9 + + - +
103Q TRP* 4.2 19.5 - + - -
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Residues in contact with GLN 37 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36P TYR* 1.3 72.1 - - - +
38P HIS* 1.3 62.9 + - - +
39P LYS* 4.1 19.2 + - + +
44P PRO* 3.3 1.4 - - - +
45P ILE* 2.6 63.9 + - + +
47P LEU* 3.5 27.8 - - + +
62P PHE* 4.1 17.4 - - - -
81P GLY 4.4 11.5 + - - -
82P ASP* 4.5 2.4 + - - +
84P ALA* 3.8 15.5 - - + -
85P ASP 3.7 3.1 - - - -
86P TYR* 3.1 28.5 + - + -
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Residues in contact with HIS 38 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36P TYR 5.4 0.2 - - - -
37P GLN* 1.3 78.3 - - - +
39P LYS* 1.3 64.6 + - - +
40P PRO* 3.3 31.2 - - + +
41P GLY 4.5 0.2 + - - -
42P GLN 3.2 27.4 + - - -
43P ALA 4.0 0.2 - - - -
44P PRO* 3.7 30.8 - - + +
84P ALA* 3.9 0.9 - - - -
85P ASP* 2.9 43.6 + - + +
87P TYR* 4.1 23.1 + - + -
39Q GLN* 3.4 37.5 + - + -
45Q LEU* 4.0 11.1 - - + +
91Q PHE* 4.8 2.2 - - - -
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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