Contacts of the strand formed by residues 31 - 39 (chain D) in PDB entry 4X7C
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 ILE 31 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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474B LEU* 4.0 20.4 - - + -
476B ARG* 4.2 15.3 - - - +
518B ASP* 3.7 27.4 - - + +
519B SER* 3.3 26.7 - - - +
521B VAL* 4.4 0.7 - - + -
525B TYR* 4.1 3.6 - - + -
29D PHE* 3.3 4.5 - - - +
30D SER* 1.3 87.5 + - - +
32D TYR* 1.3 65.7 + - - +
53D SER* 3.4 12.1 - - - +
100D TYR* 3.0 49.1 + - + +
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Residues in contact with TYR 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525B TYR* 3.7 3.8 - - - -
29D PHE 3.6 5.4 - - - -
30D SER* 3.5 16.4 - - - -
31D ILE* 1.3 76.1 - - - +
33D ALA* 1.3 71.0 + - - +
34D MET* 4.3 8.1 - - + -
51D ILE* 4.7 10.5 - - + -
52D SER* 3.5 2.6 - - - -
53D SER* 2.9 55.0 + - - -
76D ASN* 5.9 3.5 - - - -
97D ARG* 3.4 43.5 - - - +
98D GLU 3.2 15.5 - - - +
99D ASP* 4.0 2.7 - - - +
100D TYR* 3.5 8.7 - - - -
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Residues in contact with ALA 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524B PHE* 3.5 40.6 - - + +
525B TYR* 4.1 2.5 - - - -
32D TYR* 1.3 77.6 - - - +
34D MET* 1.3 62.5 + - - +
50D SER* 5.5 0.2 - - - -
51D ILE 3.3 8.1 - - - +
52D SER* 3.7 11.7 - - - +
97D ARG* 3.4 5.0 - - - +
98D GLU 2.9 31.7 + - - +
100D TYR* 3.6 10.9 - - - +
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Residues in contact with MET 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524B PHE* 3.9 5.8 - - - -
4D LEU* 3.8 14.8 - - + -
22D CYS* 3.7 42.0 - - - +
24D ALA* 4.0 7.9 - - + +
32D TYR* 4.6 7.2 - - + -
33D ALA* 1.3 72.0 - - - +
35D GLY* 1.3 57.5 + - - +
50D SER* 3.2 0.9 - - - -
51D ILE* 2.7 43.3 + - + +
69D ILE* 4.5 0.7 - - - -
76D ASN 4.4 10.1 - - - +
78D VAL* 3.9 30.3 - - + -
95D CYS* 3.8 7.2 - - - -
96D LYS 3.4 4.0 - - - +
97D ARG* 3.4 45.8 - - + +
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Residues in contact with GLY 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524B PHE* 3.7 7.5 - - - -
34D MET* 1.3 77.9 - - - +
36D TRP* 1.3 70.5 + - - -
49D ALA 3.1 12.3 - - - -
50D SER* 3.9 1.1 - - - -
69D ILE* 3.8 3.8 - - - -
78D VAL* 4.8 3.0 - - - +
95D CYS* 3.3 7.7 - - - -
96D LYS* 2.7 39.3 + - - -
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Residues in contact with TRP 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524B PHE* 4.9 0.8 - - - -
6D GLU* 4.5 9.9 - - + -
7D SER 4.9 1.1 - - - -
20D LEU* 3.5 38.8 - - + -
21D SER* 3.5 36.8 - - - -
22D CYS* 3.7 15.5 - - + -
35D GLY* 1.3 84.8 - - - -
37D TYR* 1.3 72.3 + - - +
47D LEU* 3.9 1.6 - - - +
48D VAL* 2.8 30.5 + - + -
49D ALA 2.8 20.2 + - - +
69D ILE* 3.9 13.5 - - + +
78D VAL* 4.3 10.1 - - + +
80D LEU* 3.5 42.5 - - + +
93D TYR* 4.6 5.8 - - + -
94D TYR* 3.4 10.3 - - - +
95D CYS* 3.7 27.1 - - + -
114D THR* 5.5 1.8 - - - -
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Residues in contact with TYR 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523B GLN* 5.6 6.6 + - - +
524B PHE* 3.5 34.8 - + - -
36D TRP* 1.3 80.9 - - - +
38D ARG* 1.3 60.6 + - - +
45D ARG* 3.5 46.7 + - + -
46D GLU* 3.3 21.5 - - - +
47D LEU* 3.5 26.7 - - + +
48D VAL* 4.0 2.6 - - - +
93D TYR* 3.4 4.7 - - - +
94D TYR* 2.8 56.9 + - + -
96D LYS* 3.5 26.7 - - + -
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Residues in contact with ARG 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D TYR* 1.3 74.6 - - - +
39D GLN* 1.3 60.8 + - - +
44D GLN 4.2 0.2 - - - +
45D ARG* 3.2 3.0 - - - -
46D GLU* 2.8 70.3 + - + +
47D LEU 5.4 0.8 + - - -
48D VAL* 3.6 17.4 - - + +
60D ALA* 5.9 1.0 - - - +
62D SER* 3.2 27.5 + - - -
63D VAL* 4.2 12.5 - - - +
67D PHE* 4.6 0.4 - - - -
88D GLU* 4.4 7.9 + - - +
89D ASP* 3.0 34.1 + - - +
91D ALA* 3.8 14.6 - - + -
92D VAL 3.1 11.2 - - - +
93D TYR* 2.8 39.3 + - + -
94D TYR* 4.4 2.7 - - - -
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Residues in contact with GLN 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ARG* 1.3 77.3 - - - +
40D ALA* 1.3 63.9 + - - +
41D PRO* 4.2 0.7 - - + +
42D GLY 6.0 0.2 - - - +
43D LYS 3.1 27.2 + - - +
44D GLN* 4.3 3.6 - - - +
45D ARG* 4.0 24.2 - - + +
91D ALA* 3.8 3.6 - - - -
92D VAL* 2.9 36.6 + - + +
94D TYR* 4.4 14.2 + - + -
110D ARG* 5.4 3.6 + - - -
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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