Contacts of the strand formed by residues 5 - 15 (chain D) in PDB entry 2Q6W
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 HIS 5 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3D GLU* 3.6 1.7 - - - +
4D GLU* 1.3 109.2 + - + +
6D VAL* 1.3 70.5 + - - +
26D PHE* 3.1 29.7 - + + -
27D ASP* 2.6 31.8 + - - +
17E PHE* 2.9 41.5 + - + +
83E TYR* 4.0 21.5 - + + -
91E VAL* 3.8 23.7 + - + +
124E PRO* 6.0 5.6 - - + -
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Residues in contact with VAL 6 (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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3D GLU* 2.9 44.2 - - - +
5D HIS* 1.3 76.4 - - - +
7D ILE* 1.3 69.0 + - - +
8D ILE* 3.6 28.3 + - + +
25D ASP* 3.5 1.6 - - - +
26D PHE* 3.4 4.6 - - - -
27D ASP* 3.0 32.1 + - - +
15E CYS 3.0 12.6 - - - +
16E HIS* 3.3 24.0 - - + +
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Residues in contact with ILE 7 (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 VAL* 1.3 77.9 - - - +
8D ILE* 1.3 64.1 + - - +
24D PHE* 3.6 29.8 - - + -
25D ASP 3.1 8.5 - - - +
26D PHE* 3.8 23.8 - - + -
31D ILE* 4.3 10.3 - - + -
13E SER 3.6 2.1 - - - +
14E GLU* 3.4 1.6 - - - -
15E CYS* 2.7 40.7 + - + +
17E PHE* 3.8 22.9 - - + -
78E TYR* 5.4 0.4 + - - +
82E ASN* 5.2 5.2 - - + -
83E TYR* 5.3 10.3 - - + +
25F TRP* 4.5 9.2 - - + +
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Residues in contact with ILE 8 (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 VAL* 3.6 21.3 - - + -
7D ILE* 1.3 79.1 - - - +
9D GLN* 1.3 76.5 + - - +
10D ALA* 3.8 6.2 + - + +
24D PHE* 3.0 9.3 - - - -
25D ASP* 2.8 51.5 + - + +
139D PRO* 4.7 7.9 - - + -
140D ARG 6.5 0.7 - - - -
141D GLU* 5.7 7.9 - - + -
12E LYS* 3.7 31.4 - - + +
13E SER 3.3 4.0 - - - +
14E GLU* 3.8 25.4 - - + +
16E HIS* 5.6 0.2 - - + -
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Residues in contact with GLN 9 (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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7D ILE 4.1 0.2 - - - -
8D ILE* 1.3 75.3 - - - +
10D ALA* 1.3 59.2 + - - +
11D GLU* 2.4 29.3 + - - +
22D PHE* 3.1 29.5 - - + -
23D MET 3.2 6.7 - - - +
24D PHE* 3.1 16.7 - - + -
62D ASN* 3.1 4.0 + - - -
11E ARG* 3.4 4.1 + - - +
12E LYS* 3.1 4.7 - - - -
13E SER* 2.7 39.0 + - - +
78E TYR* 2.9 21.9 + - - +
27F SER* 3.4 0.2 - - - -
28F ASP 2.8 42.9 + - - +
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Residues in contact with ALA 10 (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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8D ILE* 3.8 2.7 + - + -
9D GLN* 1.3 74.8 - - - +
11D GLU* 1.3 58.6 + - - +
12D PHE* 6.1 1.8 - - + -
21D GLU* 3.8 2.9 - - - +
22D PHE* 3.4 1.2 - - - -
23D MET* 2.7 52.4 + - + +
139D PRO* 3.8 35.4 - - + -
145D PHE* 6.2 1.1 - - + -
10E LEU* 4.6 7.2 - - + -
11E ARG 3.3 4.3 - - - +
12E LYS* 4.1 10.8 - - + -
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Residues in contact with GLU 11 (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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9D GLN* 2.4 34.5 + - - +
10D ALA* 1.3 77.9 - - - +
12D PHE* 1.3 65.7 + - - +
21D GLU 2.9 11.4 - - - +
22D PHE* 3.5 7.6 - - + -
62D ASN* 2.8 22.5 - - - +
63D ILE* 3.7 5.8 - - + -
66D ASP* 2.6 36.5 - - - +
10E LEU* 3.2 3.3 - - - +
11E ARG* 2.6 62.2 + - + +
30F ALA* 3.4 5.7 - - - +
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Residues in contact with PHE 12 (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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10D ALA* 6.0 1.6 - - + -
11D GLU* 1.3 80.3 - - - +
13D TYR* 1.3 66.4 + - - +
14D LEU* 4.5 1.1 - - + -
19D SER* 3.8 29.4 - - - -
20D GLY* 3.1 3.4 - - - -
21D GLU* 2.8 77.4 + - + +
63D ILE* 3.6 5.7 - - - +
66D ASP* 4.8 1.8 - - - -
115D PRO* 3.4 31.4 - - + -
137D PHE* 3.9 8.1 - + + -
145D PHE* 3.6 23.1 - + + -
8E LEU* 3.9 18.6 - - + -
9E GLU 2.9 11.0 - - - +
10E LEU* 3.9 10.8 - - + -
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Residues in contact with TYR 13 (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 PHE* 1.3 76.8 - - - +
14D LEU* 1.3 61.5 + - - +
15D ASN* 3.6 20.0 - - - -
18D GLN* 3.0 48.9 + - - +
19D SER 3.2 13.7 - - - -
20D GLY* 3.8 2.9 - - - -
63D ILE* 3.5 30.7 - - + +
66D ASP* 4.1 10.1 - - + +
67D LYS* 3.4 60.2 + - + +
70D LEU* 3.3 16.3 - - + +
8E LEU* 3.4 2.4 - - - +
9E GLU* 2.6 35.1 + - - +
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Residues in contact with LEU 14 (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 PHE* 4.4 2.9 - - + -
13D TYR* 1.3 75.6 - - - +
15D ASN* 1.3 55.2 + - - +
17D ASP* 3.2 20.3 + - + +
18D GLN* 2.8 31.2 + - - -
19D SER* 2.7 26.0 + - - +
70D LEU* 4.1 0.2 - - - -
114D PRO* 3.9 14.6 - - + -
115D PRO* 4.1 7.4 - - + +
116D VAL* 3.1 36.1 - - + -
6E ARG* 3.5 25.4 - - + -
7E PHE 3.2 19.1 - - - +
8E LEU* 3.7 20.6 - - + -
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Residues in contact with ASN 15 (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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13D TYR* 3.6 17.7 - - - -
14D LEU* 1.3 74.3 - - - +
16D PRO* 1.3 70.4 - - + +
17D ASP* 3.4 3.8 - - - -
18D GLN* 4.1 12.5 + - - +
67D LYS* 4.9 4.4 + - - +
70D LEU* 3.0 31.9 - - + +
71D GLU* 4.8 6.3 - - - +
74D THR* 5.1 1.8 + - - -
6E ARG* 3.2 6.2 - - - +
7E PHE* 2.7 48.3 + - + +
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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