Contacts of the strand formed by residues 55 - 66 (chain B) in PDB entry 3Q2P
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 55 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B THR* 4.1 9.2 - - + -
46B ILE 3.8 3.1 - - - -
47B TYR* 3.9 22.9 - - + -
53B ARG 3.7 3.8 + - - +
54B GLU* 1.3 78.6 - - - +
56B LYS* 1.3 62.3 + - - +
57B GLY 3.9 12.6 - - - +
58B TYR* 3.8 26.9 - - + +
79B TYR* 3.3 57.8 - - + +
80B LYS* 5.9 0.5 - - - +
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Residues in contact with LYS 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ILE* 2.7 34.8 + - + +
48B GLU* 3.1 44.3 + - + +
54B GLU* 3.3 2.8 + - - -
55B ILE* 1.3 74.1 - - - +
57B GLY* 1.3 56.3 + - - +
78B ASP* 4.0 9.6 - - - +
79B TYR* 3.0 21.8 + - - +
80B LYS* 4.8 1.9 + - - +
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Residues in contact with GLY 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B THR* 3.9 0.2 - - - -
46B ILE* 3.0 33.3 + - - +
55B ILE* 3.7 4.2 - - - +
56B LYS* 1.3 82.6 - - - +
58B TYR* 1.3 73.1 + - - -
77B GLU 3.2 13.0 - - - -
78B ASP* 4.3 1.1 - - - -
79B TYR* 3.8 8.3 - - - -
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Residues in contact with TYR 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LYS* 3.6 36.0 + - - -
44B LYS 3.2 8.1 - - - +
45B THR* 3.7 23.6 - - + -
46B ILE* 4.3 3.2 - - - +
55B ILE* 3.8 16.7 - - + +
57B GLY* 1.3 78.6 - - - -
59B GLU* 1.3 66.4 + - - +
60B TYR* 3.8 24.7 - - + -
75B ILE 4.6 0.2 - - - -
76B SER* 3.3 4.9 - - - -
77B GLU* 2.7 55.9 + - + +
79B TYR* 3.5 39.1 - + - -
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Residues in contact with GLU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A PRO 4.4 11.8 - - - -
3B TRP* 4.2 6.2 - - + -
42B MET 3.7 0.5 - - - +
43B LYS* 3.4 3.3 - - - +
44B LYS* 2.6 64.7 + - + +
46B ILE* 3.7 21.0 - - + +
58B TYR* 1.3 80.3 - - - +
60B TYR* 1.3 64.4 + - - +
61B GLN 4.3 0.4 - - - -
74B ASP* 3.5 24.1 - - - +
75B ILE 3.3 6.5 - - - +
76B SER* 4.5 7.8 - - - -
87B LEU* 4.1 18.0 - - - +
88B ARG* 5.1 0.5 + - - -
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Residues in contact with TYR 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B TRP* 5.6 0.4 - - - -
6B ILE* 4.0 15.0 - - + -
11B PHE* 3.7 18.1 - + - -
15B LEU* 3.7 33.9 - - + -
42B MET 3.2 4.5 - - - -
43B LYS* 3.5 45.0 + - + -
58B TYR* 3.8 29.9 - - + -
59B GLU* 1.3 75.1 - - - +
61B GLN* 1.3 60.0 + - - +
62B LEU* 3.7 19.4 + - + +
73B ALA 3.5 1.2 - - - +
74B ASP* 2.9 8.5 - - - +
75B ILE* 2.8 51.0 + - + +
77B GLU* 3.4 29.2 + - + -
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Residues in contact with GLN 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A PRO* 5.7 0.6 - - - +
63A TYR* 2.8 31.2 + - - -
72A ARG* 5.7 1.4 + - - -
96A PRO* 4.2 16.2 - - - +
3B TRP* 4.9 11.2 - - + -
40B PRO 4.3 2.1 - - - +
41B CYS* 3.6 3.3 - - - -
42B MET* 3.0 52.5 + - + +
59B GLU 4.3 0.2 - - - -
60B TYR* 1.3 70.1 - - - +
62B LEU* 1.3 62.9 + - - +
72B ARG* 3.3 33.1 + - + +
73B ALA 3.2 6.3 - - - +
74B ASP* 3.7 25.7 + - + +
88B ARG* 5.3 3.6 - - - +
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Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 5.7 0.4 - - + -
12B THR* 4.0 11.9 - - + +
15B LEU* 3.6 16.8 - - + -
16B ALA* 3.4 41.3 - - + +
37B ALA* 5.5 0.2 - - + -
40B PRO 4.9 0.2 - - - -
41B CYS* 3.7 25.6 - - + -
42B MET 4.9 0.2 - - - +
60B TYR* 3.7 25.1 - - + -
61B GLN* 1.3 81.4 - - - +
63B TYR* 1.3 67.9 + - - +
64B VAL* 4.1 0.6 + - + -
72B ARG* 3.3 11.1 - - - +
73B ALA* 2.8 40.4 + - + +
75B ILE* 3.9 14.4 - - + -
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Residues in contact with TYR 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLN* 2.8 25.6 + - - -
72A ARG* 5.1 0.5 + - - -
37B ALA* 3.4 7.8 - - - +
38B ILE* 3.2 43.4 + - + +
40B PRO* 3.5 45.3 - - + -
41B CYS* 3.9 4.4 - - - -
62B LEU* 1.3 75.4 - - - +
64B VAL* 1.3 60.9 + - - +
70B LEU* 3.8 22.4 - - + -
71B PHE 3.4 1.8 - - - -
72B ARG* 2.9 45.6 + - - -
93B VAL* 4.0 16.4 - - + -
94B PRO 4.2 11.3 + - - -
96B PRO* 3.8 15.8 - - + +
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Residues in contact with VAL 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ALA* 3.7 30.7 - - + +
20B VAL* 4.1 9.6 - - + -
34B PHE* 3.9 13.5 - - + -
36B LYS 3.4 8.7 - - - +
62B LEU* 5.3 1.3 - - + -
63B TYR* 1.3 77.1 - - - +
65B TYR* 1.3 74.6 + - - +
66B ALA 3.7 0.5 + - - -
69B LYS 3.4 1.2 - - - +
70B LEU* 3.5 5.9 - - - +
71B PHE* 2.9 53.6 + - + +
73B ALA* 4.6 12.1 - - + -
89B PHE* 4.4 18.2 - - + -
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Residues in contact with TYR 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ASN* 2.8 48.2 + - + +
36B LYS* 2.7 22.1 + - + +
38B ILE* 4.0 38.2 - - + +
64B VAL* 1.3 76.9 - - - +
66B ALA* 1.3 53.5 + - - +
68B ASP* 4.1 9.2 - - - -
69B LYS 3.1 24.7 - - - -
70B LEU* 3.6 32.5 - - + +
95B PRO* 4.7 9.7 - - - +
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Residues in contact with ALA 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B VAL* 4.1 24.5 - - + -
32B LEU* 4.1 15.0 - - + +
33B THR 3.2 16.8 - - - +
34B PHE* 4.2 0.4 - - - -
35B ASN* 3.3 0.6 + - - -
64B VAL 3.7 1.2 + - - +
65B TYR* 1.3 76.3 - - - +
67B SER* 1.3 74.4 + - - +
68B ASP 3.3 0.2 - - - -
69B LYS* 2.8 15.8 + - - +
71B PHE* 3.3 22.4 - - + -
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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