Contacts of the strand formed by residues 54 - 67 (chain A) in PDB entry 6Q3W
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 PRO 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ARG* 3.6 26.7 - - - -
38A VAL 3.3 7.0 - - - +
39A ASN* 3.5 10.3 - - - +
40A LEU* 4.8 0.2 - - - -
52A VAL* 3.4 13.0 - - + +
53A LEU* 1.3 92.8 - - - +
55A MET* 1.3 60.3 + - - +
185A MET* 4.0 13.2 - - + -
189A ILE* 3.7 23.6 - - + -
198A ALA* 3.5 3.3 - - - -
199A LEU* 2.8 41.3 + - - +
201A ILE* 4.0 6.1 - - + -
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Residues in contact with MET 55 (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 ARG* 3.2 4.2 - - - +
38A VAL* 2.9 39.6 + - + -
40A LEU* 4.4 9.8 - - + +
54A PRO* 1.3 75.8 - - - +
56A ALA* 1.3 67.6 + - - +
57A LEU* 4.2 13.0 - - + -
189A ILE* 3.8 9.0 - - - -
197A HIS 4.1 5.2 - - - +
198A ALA* 3.9 19.3 - - + +
213A LEU* 3.8 25.1 - - + -
220A VAL* 4.1 22.9 - - + -
381A SER 3.3 27.6 - - - +
382A GLN 3.8 14.8 - - - +
383A ALA* 3.8 12.1 - - + +
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Residues in contact with ALA 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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35A PRO* 3.6 25.4 - - + -
36A GLY 3.7 5.8 - - - -
55A MET* 1.3 81.6 - - - +
57A LEU* 1.3 60.7 + - - +
189A ILE* 3.7 13.6 - - - +
193A GLY* 4.1 13.2 - - - -
197A HIS 4.9 2.2 + - - -
382A GLN 3.6 5.5 - - - +
384A ALA 2.9 43.5 + - - +
385A ASP 3.6 3.1 - - - +
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Residues in contact with LEU 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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35A PRO* 3.2 20.1 - - - +
36A GLY* 3.0 14.3 + - - +
37A ARG* 3.5 33.0 - - - +
38A VAL* 3.8 17.0 - - + +
55A MET* 4.2 3.8 - - + -
56A ALA* 1.3 78.5 - - - +
58A GLU* 1.3 63.9 + - - +
59A LEU* 3.1 20.1 - - + +
60A MET* 5.1 1.4 - - - +
139A LEU* 3.9 26.9 - - + -
222A ILE* 3.6 26.9 - - + -
381A SER* 3.5 19.5 - - - +
384A ALA* 3.3 11.2 - - - +
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Residues in contact with GLU 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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6A GLN* 3.1 35.6 - - + +
7A PRO 4.4 7.3 - - - +
57A LEU* 1.3 71.4 - - - +
59A LEU* 1.3 63.8 + - - +
60A MET* 3.3 27.8 + - + +
132A SER* 4.2 1.9 + - - -
195A LYS* 5.5 4.0 + - - -
380A LEU 4.5 2.3 - - - +
381A SER* 3.5 9.8 + - - +
382A GLN* 4.1 27.4 + - + +
384A ALA* 3.8 15.9 - - + +
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Residues in contact with LEU 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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5A ARG 5.2 1.6 - - - +
6A GLN* 3.8 34.5 - - + +
7A PRO* 5.5 0.2 - - + -
35A PRO* 3.4 0.2 - - - +
36A GLY 2.9 22.1 + - - +
57A LEU* 3.3 24.6 - - + +
58A GLU* 1.3 76.8 - - - +
60A MET* 1.3 58.2 + - - +
132A SER* 3.5 24.5 - - - +
133A VAL* 3.5 15.0 - - + -
134A PRO* 3.8 20.4 - - + -
139A LEU* 3.8 19.5 - - + -
379A TYR* 3.7 33.4 - - + -
381A SER* 6.3 0.4 - - - -
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Residues in contact with MET 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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7A PRO 4.5 4.3 - - - +
8A GLN* 5.3 0.4 - - - -
9A VAL* 3.7 49.8 - - + +
12A LEU* 3.6 16.5 - - + +
33A SER* 3.9 14.1 - - - -
34A ALA 3.5 14.8 - - - +
35A PRO* 3.9 7.2 - - + -
57A LEU 5.4 1.1 - - - +
58A GLU* 3.3 24.5 - - + +
59A LEU* 1.3 75.3 - - - +
61A THR* 1.3 60.0 + - - +
62A VAL* 4.0 7.0 - - + -
131A SER* 3.3 1.9 - - - -
132A SER* 2.9 34.0 + - - -
133A VAL* 3.4 10.3 - - - +
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Residues in contact with THR 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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33A SER* 3.2 3.8 - - - -
34A ALA 2.8 34.3 + - - -
60A MET* 1.3 71.8 - - - +
62A VAL* 1.3 65.2 + - - +
63A LEU* 4.0 13.9 - - + -
129A VAL* 3.9 21.1 - - + -
130A VAL 3.3 12.1 - - - +
131A SER* 3.0 18.3 + - - -
141A SER* 4.2 2.1 + - - -
144A SER* 2.8 31.5 + - - -
145A LEU* 4.1 16.4 + - + +
148A ALA* 4.1 4.2 - - + +
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Residues in contact with VAL 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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9A VAL* 4.3 7.2 - - + -
12A LEU* 3.9 20.0 - - + -
13A LEU* 4.4 14.8 - - + +
16A ALA* 4.3 4.4 - - + +
31A ALA* 5.4 0.2 - - + -
32A VAL 3.3 11.0 - - - +
33A SER* 3.8 18.4 - - - -
60A MET* 4.0 13.4 + - + -
61A THR* 1.3 78.3 - - - +
63A LEU* 1.3 72.3 + - - +
64A VAL* 4.2 13.9 - - + -
128A VAL 3.7 1.2 - - - +
129A VAL* 3.6 2.8 - - - -
130A VAL* 2.7 52.5 + - + +
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Residues in contact with LEU 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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31A ALA* 3.3 3.1 - - - +
32A VAL* 2.9 45.5 + - + +
61A THR* 4.0 4.2 + - + -
62A VAL* 1.3 75.5 - - - +
64A VAL* 1.3 63.2 + - - +
75A LEU* 6.0 1.1 - - + -
110A VAL* 5.7 3.1 - - + -
125A PHE* 5.4 3.4 - - + -
127A ALA* 4.4 15.9 - - + -
128A VAL 3.4 4.0 - - - +
129A VAL* 3.8 30.5 - - + -
145A LEU* 3.9 14.4 - - + -
148A ALA* 3.7 22.4 - - + -
149A THR* 4.2 26.2 - - + +
152A PHE* 4.4 19.2 - - + -
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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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13A LEU* 3.7 26.7 - - + -
16A ALA* 3.3 48.0 - - + +
17A ARG* 4.1 5.2 - - + +
20A PHE* 3.8 16.2 - - + -
28A PRO* 4.1 9.9 - - + -
30A LEU 3.2 7.6 - - - +
31A ALA* 3.9 6.3 - - + -
62A VAL* 4.2 2.5 - - + -
63A LEU* 1.3 80.8 - - - +
65A GLY* 1.3 58.7 + - - +
127A ALA* 3.2 3.6 - - - +
128A VAL* 2.9 34.3 + - + -
152A PHE* 4.5 3.1 - - - -
392A LEU* 4.6 0.4 - - + -
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Residues in contact with GLY 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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20A PHE* 3.5 9.6 - - - -
28A PRO* 3.8 2.6 - - - +
29A GLU 3.1 4.2 + - - -
30A LEU* 2.9 38.2 + - - +
64A VAL* 1.3 75.2 - - - +
66A SER* 1.3 64.3 + - - -
126A SER 3.0 13.0 - - - -
152A PHE* 3.8 15.0 - - - -
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Residues in contact with SER 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 PHE* 3.7 12.4 - - - -
27A GLU 3.9 2.9 + - - -
28A PRO* 3.5 8.0 - - - +
29A GLU* 3.2 31.3 + - - +
65A GLY* 1.3 76.3 - - - -
67A PRO* 1.3 77.3 - - - +
68A ARG* 4.4 0.3 - - - +
125A PHE* 3.2 5.5 - - - +
126A SER* 2.9 32.8 + - - -
152A PHE* 4.0 4.0 - - - -
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Residues in contact with PRO 67 (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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29A GLU* 3.7 21.9 - - + +
30A LEU* 4.6 7.6 - - + -
66A SER* 1.3 94.2 - - - +
68A ARG* 1.3 63.4 + - - +
123A PRO* 4.4 11.2 - - + -
124A GLY 3.5 8.1 - - - +
125A PHE* 4.1 3.6 - - + -
156A LEU* 3.8 24.2 - - + -
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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