Contacts of the strand formed by residues 55 - 66 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45D THR* 4.2 8.1 - - + -
46D ILE 3.7 5.8 - - - +
47D TYR* 3.8 22.0 - - + +
53D ARG 4.6 2.9 - - - +
54D GLU* 1.3 74.0 - - - +
56D LYS* 1.3 62.5 + - - +
57D GLY 3.8 17.0 - - - +
58D TYR* 4.0 14.6 - - + +
79D TYR* 3.4 66.3 - - + +
80D LYS* 5.6 2.3 - - - +
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Residues in contact with LYS 56 (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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46D ILE* 2.8 34.2 + - + +
47D TYR 4.6 7.9 - - - +
48D GLU* 4.7 12.1 - - + +
54D GLU* 3.3 3.9 + - - +
55D ILE* 1.3 72.8 - - - +
57D GLY* 1.3 63.4 + - - +
78D ASP* 3.2 24.4 - - - +
79D TYR* 3.3 7.5 + - - +
80D LYS* 4.8 3.1 + - - +
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Residues in contact with GLY 57 (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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46D ILE* 3.1 29.2 + - - +
55D ILE* 3.7 4.8 - - - +
56D LYS* 1.3 86.4 - - - +
58D TYR* 1.3 72.7 + - - -
77D GLU 3.4 10.8 - - - -
78D ASP* 4.2 1.6 - - - -
79D TYR* 3.6 11.2 - - - -
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Residues in contact with TYR 58 (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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43D LYS* 3.5 33.7 + - - -
44D LYS 3.3 8.5 - - - +
45D THR* 3.8 26.5 - - + -
46D ILE* 4.5 7.4 - - - +
55D ILE* 4.0 10.4 - - + +
57D GLY* 1.3 79.3 - - - -
59D GLU* 1.3 62.9 + - - +
60D TYR* 4.1 22.2 - - + -
76D SER* 3.4 6.2 - - - -
77D GLU* 2.8 57.2 + - + +
79D TYR* 3.4 43.7 - + - -
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Residues in contact with GLU 59 (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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95C PRO 5.2 1.0 - - - +
96C PRO* 3.1 24.8 - - - +
3D TRP* 4.1 5.2 - - + -
42D MET 3.9 0.2 - - - +
43D LYS* 3.4 4.7 - - - +
44D LYS* 2.7 65.7 + - + +
46D ILE* 4.3 10.7 - - + +
58D TYR* 1.3 75.8 - - - +
60D TYR* 1.3 66.2 + - - +
74D ASP* 2.6 38.3 - - - +
75D ILE 3.2 7.9 - - - +
76D SER* 4.8 1.1 - - - -
87D LEU* 4.1 14.1 - - + +
88D ARG* 5.9 1.0 + - - -
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Residues in contact with TYR 60 (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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6D ILE* 4.1 13.2 - - + -
11D PHE* 3.6 17.4 - + - -
15D LEU* 3.4 37.2 - - + -
42D MET 3.3 14.6 - - - +
43D LYS* 3.5 44.0 + - + -
58D TYR* 4.1 20.6 - - + +
59D GLU* 1.3 77.0 - - - +
61D GLN* 1.3 61.5 + - - +
62D LEU* 3.3 19.7 - - + +
73D ALA 3.4 1.4 - - - +
74D ASP* 3.2 8.3 - - - +
75D ILE* 2.7 50.3 + - + +
77D GLU* 4.1 27.2 + - + -
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Residues in contact with GLN 61 (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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40C PRO* 4.7 1.6 - - - +
61C GLN* 5.2 2.8 - - - +
63C TYR* 2.9 22.2 + - - -
96C PRO* 3.3 21.0 - - - +
3D TRP* 3.7 21.7 - - + -
40D PRO 4.3 1.6 - - - +
41D CYS* 3.5 4.9 - - - -
42D MET* 3.0 62.6 + - + +
60D TYR* 1.3 70.1 - - - +
62D LEU* 1.3 62.5 + - - +
72D ARG* 2.7 41.4 + - - +
73D ALA 3.4 4.3 - - - -
74D ASP* 3.2 11.8 - - - +
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Residues in contact with LEU 62 (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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12D THR* 4.0 8.5 - - + +
15D LEU* 3.7 14.4 - - + -
16D ALA* 3.4 43.3 - - + +
19D ALA* 5.4 0.2 - - + -
37D ALA* 5.3 0.4 - - + -
41D CYS* 3.9 19.5 - - + -
42D MET 5.1 0.2 - - - +
60D TYR* 3.3 35.2 - - + +
61D GLN* 1.3 80.3 - - - +
63D TYR* 1.3 63.7 + - - +
64D VAL* 3.9 11.2 - - + -
72D ARG* 3.3 8.4 - - - +
73D ALA* 2.8 38.2 + - + +
75D ILE* 4.0 11.7 - - + -
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Residues in contact with TYR 63 (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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42C MET* 5.5 0.7 - - + -
61C GLN* 3.0 29.9 + - - -
72C ARG* 3.2 14.6 + - - -
37D ALA* 3.3 6.2 - - - +
38D ILE* 3.0 47.4 + - + +
40D PRO* 3.6 30.5 - - + -
41D CYS* 4.0 5.1 - - - -
42D MET* 6.2 2.0 - - + -
62D LEU* 1.3 74.6 - - - +
64D VAL* 1.3 61.5 + - - +
70D LEU* 3.7 27.6 - - + -
71D PHE 3.3 2.0 - - - -
72D ARG* 3.9 24.4 - - + +
93D VAL* 4.0 17.9 - - + -
94D PRO 4.2 6.7 + - - -
96D PRO* 3.8 23.8 - - + +
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Residues in contact with VAL 64 (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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16D ALA* 3.7 24.2 - - + +
19D ALA* 4.9 1.8 - - + -
20D VAL* 3.8 27.1 - - + -
34D PHE* 3.9 14.8 - - + -
36D LYS 3.6 7.2 - - - +
62D LEU* 4.1 15.9 - - + +
63D TYR* 1.3 78.3 - - - +
65D TYR* 1.3 71.2 + - - +
66D ALA* 3.7 1.5 + - + +
69D LYS 3.6 1.0 - - - +
70D LEU* 3.5 4.8 - - - +
71D PHE* 2.7 42.6 + - + +
73D ALA* 4.4 15.3 - - + -
89D PHE* 5.0 6.5 - - + -
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Residues in contact with TYR 65 (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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31B ARG* 3.5 49.9 + - + +
33B THR* 4.1 11.8 + - - -
35D ASN* 2.8 50.2 + - + +
36D LYS* 2.7 26.9 + - + +
38D ILE* 3.9 39.2 - - + +
63D TYR 4.3 0.2 - - - -
64D VAL* 1.3 75.8 - - - +
66D ALA* 1.3 53.6 + - - +
68D ASP* 4.2 10.5 - - - -
69D LYS 3.4 16.4 - - - -
70D LEU* 3.7 33.7 - - + +
95D PRO* 5.0 5.2 - - - +
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Residues in contact with ALA 66 (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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20D VAL* 4.0 24.2 - - + -
32D LEU* 4.1 19.4 - - + +
33D THR 3.1 11.4 - - - +
35D ASN* 2.9 2.4 + - - -
64D VAL* 3.7 2.1 + - + -
65D TYR* 1.3 74.6 - - - +
67D SER* 1.3 73.7 + - - +
68D ASP 3.0 0.9 + - - -
69D LYS* 3.0 18.2 + - - +
71D PHE* 3.6 21.9 - - + -
89D PHE* 5.1 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