Contacts of the strand formed by residues 55 - 66 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A THR* 4.5 5.4 - - + -
46A ILE 3.9 6.1 - - - +
47A TYR* 4.1 21.5 - - + +
48A GLU* 5.1 1.2 - - - +
53A ARG* 4.0 8.0 + - + +
54A GLU* 1.3 74.2 - - - +
56A LYS* 1.3 60.6 + - - +
57A GLY 3.7 13.9 - - - +
58A TYR* 3.7 28.0 - - + +
79A TYR* 3.3 58.5 - - + +
80A LYS* 5.0 8.5 + - - +
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Residues in contact with LYS 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE* 3.0 39.8 + - + +
47A TYR 4.3 11.0 + - - +
48A GLU* 4.3 28.6 + - - +
49A ASN* 5.9 2.2 - - - +
54A GLU 3.5 2.0 + - - -
55A ILE* 1.3 73.3 - - - +
57A GLY* 1.3 59.9 + - - +
78A ASP* 3.8 12.4 - - - +
79A TYR* 3.1 19.6 + - - +
80A LYS* 4.6 1.1 + - - +
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Residues in contact with GLY 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A THR* 4.0 0.2 - - - -
46A ILE* 3.1 31.7 + - - +
55A ILE* 3.7 2.9 - - - +
56A LYS* 1.3 81.2 - - - +
58A TYR* 1.3 72.4 + - - -
77A GLU 3.2 12.3 - - - -
78A ASP* 4.4 0.2 - - - -
79A TYR* 3.7 11.2 - - - -
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Residues in contact with TYR 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LYS* 3.6 31.6 - - - -
44A LYS 3.3 8.3 - - - +
45A THR* 3.4 36.8 - - + -
46A ILE* 4.9 5.7 - - - +
55A ILE* 3.7 15.5 - - + +
57A GLY* 1.3 80.6 - - - -
59A GLU* 1.3 64.6 + - - +
60A TYR* 4.3 11.4 - - + +
76A SER* 3.4 5.0 - - - -
77A GLU* 2.7 61.1 + - + +
79A TYR* 3.3 39.9 - + + -
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Residues in contact with GLU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A TRP* 4.1 8.6 - - + -
43A LYS* 3.4 3.8 - - - +
44A LYS* 2.7 58.9 + - + +
46A ILE* 4.0 17.2 - - + +
58A TYR* 1.3 78.3 - - - +
60A TYR* 1.3 65.2 + - - +
74A ASP* 5.0 7.3 - - + +
75A ILE 3.2 15.3 - - - +
76A SER* 3.9 11.0 - - - -
87A LEU* 3.9 20.0 - - + +
88A ARG* 5.0 5.4 + - - -
96B PRO* 4.8 14.0 - - - +
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Residues in contact with TYR 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A TRP* 4.9 0.4 - - - -
6A ILE* 4.3 9.9 - - + -
11A PHE* 3.5 12.6 - + - -
15A LEU* 3.5 39.5 - - + -
42A MET 3.2 6.3 - - - -
43A LYS* 3.4 55.6 + - + -
58A TYR* 4.3 7.7 - - + +
59A GLU* 1.3 76.0 - - - +
61A GLN* 1.3 63.4 + - - +
62A LEU* 3.3 21.3 - - + -
73A ALA 3.6 0.7 - - - +
74A ASP* 3.1 8.3 - - - +
75A ILE* 2.8 49.8 + - + +
77A GLU* 3.0 38.8 + - + -
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Residues in contact with GLN 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A TRP* 4.0 16.0 - - + -
40A PRO 4.2 2.4 - - - +
41A CYS* 3.7 3.1 - - - -
42A MET* 3.0 59.1 + - + +
60A TYR* 1.3 72.6 - - - +
62A LEU* 1.3 63.5 + - - +
63A TYR* 5.6 0.3 - - - -
72A ARG* 3.2 31.0 + - - +
73A ALA 3.4 4.5 - - - -
74A ASP* 3.6 21.2 - - - +
42B MET* 5.3 0.6 - - - +
63B TYR* 2.8 22.0 + - - -
72B ARG* 3.4 18.0 - - - +
96B PRO* 4.3 10.6 - - - +
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ILE* 6.1 1.8 - - + -
12A THR* 4.2 10.5 - - + +
15A LEU* 3.7 29.2 - - + -
16A ALA* 3.8 22.9 - - + +
19A ALA* 5.5 0.7 - - + -
41A CYS* 4.2 22.9 - - + -
42A MET 4.4 2.2 - - - +
60A TYR* 3.3 28.9 - - + -
61A GLN* 1.3 82.7 - - - +
63A TYR* 1.3 70.0 + - - +
64A VAL* 5.3 1.3 - - + -
72A ARG* 3.3 7.8 + - - -
73A ALA* 2.8 45.6 + - + +
75A ILE* 3.8 14.8 - - + -
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Residues in contact with TYR 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ALA* 3.4 7.4 - - - +
38A ILE* 3.1 47.8 + - + +
40A PRO* 3.4 42.6 - - + -
41A CYS* 4.2 5.5 - - - -
61A GLN 5.6 0.7 - - - -
62A LEU* 1.3 73.1 - - - +
64A VAL* 1.3 60.9 + - - +
70A LEU* 4.1 21.5 - - + -
71A PHE 3.4 4.0 - - - -
72A ARG* 3.5 35.9 - - + +
93A VAL* 3.9 14.9 - - + +
94A PRO 4.3 3.1 + - - -
96A PRO* 3.9 19.7 - - + +
42B MET* 5.9 1.8 - - + -
61B GLN* 2.8 33.4 + - - -
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Residues in contact with VAL 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ALA* 3.9 24.5 - - + +
19A ALA* 5.0 3.8 - - + -
20A VAL* 3.9 21.8 - - + -
34A PHE* 4.1 4.9 - - + -
36A LYS 3.6 9.2 - - - +
62A LEU* 4.7 2.9 - - + +
63A TYR* 1.3 76.9 - - - +
65A TYR* 1.3 74.0 + - - +
66A ALA 3.7 0.9 + - - -
69A LYS 3.6 1.4 - - - +
70A LEU* 3.8 5.3 - - - +
71A PHE* 2.8 46.8 + - + +
73A ALA* 4.4 12.8 - - + +
89A PHE* 4.1 26.0 - - + -
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Residues in contact with TYR 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ASN* 2.8 46.5 + - + +
36A LYS* 3.0 33.7 + - + +
38A ILE* 4.0 22.8 - - + +
64A VAL* 1.3 76.0 - - - +
66A ALA* 1.3 55.6 + - - +
68A ASP* 4.0 12.3 - - - -
69A LYS 3.3 22.0 - - - -
70A LEU* 3.7 42.1 - - + +
95A PRO* 4.9 9.9 - - - +
97A NA 4.0 7.0 - - - -
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Residues in contact with ALA 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A VAL* 3.9 24.7 - - + -
32A LEU* 3.9 25.4 - - + -
33A THR 3.2 13.7 - - - +
35A ASN* 3.5 0.4 - - - -
64A VAL 3.7 2.1 + - - +
65A TYR* 1.3 74.9 - - - +
67A SER* 1.3 71.9 + - - +
68A ASP 3.0 1.1 - - - -
69A LYS* 2.9 18.9 + - - +
71A PHE* 3.7 13.5 - - + -
89A PHE* 5.2 0.4 - - + -
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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