Contacts of the strand formed by residues 7 - 18 (chain E) 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 PHE 7 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D LEU* 3.2 5.3 - - - +
15D ASN* 2.7 57.0 + - + +
16D PRO* 5.0 1.6 - - + -
70D LEU* 3.4 9.3 - - + +
74D THR* 3.5 36.6 - - + +
79D TYR* 3.2 44.4 - + + -
80D THR 3.3 18.6 - - - -
81D PRO* 3.6 6.3 - - + -
5E PRO* 3.8 36.3 - - + -
6E ARG* 1.3 75.8 - - - +
8E LEU* 1.3 61.7 + - - +
32E HIS* 4.0 4.0 - + - +
33E ASN* 3.5 2.9 - - - -
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Residues in contact with LEU 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D PHE* 3.9 13.9 - - + -
13D TYR 3.4 6.7 - - - +
14D LEU* 3.7 24.0 - - + -
70D LEU* 3.8 3.1 - - - -
82D ILE* 3.5 33.2 - - + -
113D THR* 3.9 10.8 - - - +
115D PRO* 3.5 26.2 - - + -
143D HIS 5.4 1.1 - - - +
145D PHE* 4.0 15.5 - - + -
7E PHE* 1.3 74.5 - - - +
9E GLU* 1.3 65.2 - - - +
10E LEU* 4.6 8.1 - - + +
31E PHE 3.8 0.2 - - - +
32E HIS* 3.1 9.0 + - - -
33E ASN* 2.5 46.7 + - - +
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Residues in contact with GLU 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D PHE* 2.9 5.5 - - - +
13D TYR 2.6 38.8 + - - +
66D ASP* 3.3 38.1 - - + +
69D ASN* 3.5 18.1 - - + +
70D LEU* 3.4 18.6 - - + +
73D MET* 3.2 20.8 - - - +
8E LEU* 1.3 71.4 - - - +
10E LEU* 1.3 63.9 + - - +
30E TYR* 5.4 4.5 - - + +
31E PHE 3.5 6.4 - - - +
32E HIS* 2.6 33.5 - - - -
37E PHE* 3.5 19.8 - - - -
33F LEU* 4.1 2.3 - - - +
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Residues in contact with LEU 10 (chain E).
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* 4.6 5.4 - - + -
11D GLU 3.2 22.0 - - - +
12D PHE* 3.9 14.1 - - + -
66D ASP* 5.5 0.7 - - - -
139D PRO* 5.7 0.2 - - + -
143D HIS* 4.1 20.6 - - + +
144D LEU 5.8 0.2 - - - +
145D PHE* 4.3 20.2 - - + -
8E LEU* 3.9 12.5 - - + -
9E GLU* 1.3 77.1 - - - +
11E ARG* 1.3 73.1 + - - +
12E LYS* 4.0 24.9 - - + +
30E TYR* 3.6 2.6 - - - +
31E PHE* 2.8 66.7 + - + +
33E ASN 5.4 1.6 - - - +
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Residues in contact with ARG 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D GLN* 3.4 4.1 - - - +
10D ALA* 3.3 3.3 - - - -
11D GLU* 2.6 81.6 + - + +
66D ASP* 3.9 18.2 - - - +
10E LEU* 1.3 78.3 - - - +
12E LYS* 1.3 63.6 + - - +
13E SER* 2.9 27.9 + - - +
28E ASP* 2.8 24.2 + - - +
29E ARG 3.2 15.9 - - - +
30E TYR* 3.5 31.8 + - + -
71E LYS* 3.6 1.2 - - - +
28F ASP* 3.1 27.2 + - - -
29F GLU 3.1 15.9 + - - -
30F ALA* 3.8 8.5 - - - +
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Residues in contact with LYS 12 (chain E).
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* 3.7 22.9 - - + +
9D GLN 3.1 3.1 - - - -
10D ALA* 4.1 7.2 - - + -
139D PRO* 3.7 22.0 - - - +
140D ARG 2.6 32.5 + - - +
141D GLU* 4.2 7.7 + - - +
143D HIS* 4.2 9.5 - - - +
144D LEU 5.7 0.4 - - - -
10E LEU* 4.0 21.1 - - + -
11E ARG* 1.3 78.7 - - - +
13E SER* 1.4 59.1 + - - +
14E GLU* 3.8 19.8 + - - +
27E LEU 3.4 3.1 - - - +
28E ASP* 4.4 1.6 - - - -
29E ARG* 2.8 41.8 + - + +
31E PHE* 3.8 22.0 - - + -
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Residues in contact with SER 13 (chain E).
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 3.6 1.6 - - - +
8D ILE* 3.3 2.1 - - - -
9D GLN* 2.7 37.3 + - - +
11E ARG* 2.9 35.2 + - - -
12E LYS* 1.4 69.8 - - - +
14E GLU* 1.3 60.5 + - - +
26E TYR* 3.9 4.9 - - - -
27E LEU 3.0 5.8 - - - -
28E ASP* 4.2 1.6 - - - +
78E TYR* 3.4 21.0 + - - -
28F ASP* 3.0 24.0 + - - +
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Residues in contact with GLU 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D ILE 3.4 4.5 - - - -
8D ILE* 3.8 20.5 - - + +
141D GLU* 4.2 6.4 - - - +
12E LYS* 3.8 28.5 + - + +
13E SER* 1.3 77.4 - - - +
15E CYS* 1.3 62.4 + - - +
16E HIS* 2.7 31.7 + - + +
25E ARG 3.3 0.9 - - - +
26E TYR* 3.2 8.7 - - - -
27E LEU* 2.6 49.7 + - + +
29E ARG* 2.9 36.9 + - - -
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Residues in contact with CYS 15 (chain E).
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* 3.0 6.8 - - - +
7D ILE* 2.7 41.1 + - + +
14E GLU* 1.3 73.4 - - - +
16E HIS* 1.3 61.9 + - - +
17E PHE* 3.3 25.5 - - + -
25E ARG 3.3 4.5 - - - -
78E TYR* 3.3 23.6 - - - -
79E CYS* 2.2 48.7 - - + -
82E ASN* 6.0 1.3 - - - -
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Residues in contact with HIS 16 (chain E).
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* 2.6 28.6 + - - +
5D HIS 3.5 3.1 - - - -
6D VAL* 3.3 20.7 - - + +
8D ILE* 5.6 0.2 - - + -
141D GLU* 5.0 8.3 - - + -
14E GLU* 2.7 40.0 + - + +
15E CYS* 1.3 78.1 - - - +
17E PHE* 1.3 59.4 + - - +
18E PHE* 3.6 16.5 - + + -
23E ARG 3.5 1.0 - - - +
24E VAL* 3.1 6.6 - - - +
25E ARG* 2.7 53.9 + - + +
27E LEU* 4.1 16.5 - - + +
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Residues in contact with PHE 17 (chain E).
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* 3.6 2.1 - - - +
4D GLU* 2.7 32.3 + - - -
5D HIS* 2.9 26.6 + - + +
6D VAL* 4.4 0.2 - - - -
7D ILE* 3.8 19.3 - - + -
15E CYS* 3.3 38.1 - - + -
16E HIS* 1.3 72.6 - - - +
18E PHE* 1.3 55.3 + - - +
20E GLY 3.5 11.4 - - - +
21E THR* 3.8 7.0 - - - -
23E ARG 3.4 2.5 - - - -
24E VAL* 3.5 28.9 - - + -
79E CYS* 3.1 34.5 - - - -
83E TYR* 3.4 37.7 - + + -
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Residues in contact with PHE 18 (chain E).
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* 3.1 48.5 - - + +
4D GLU* 4.2 5.8 - - - +
16E HIS* 3.6 27.1 - + + -
17E PHE* 1.3 75.0 - - - +
19E ASN* 1.3 70.6 - - - +
20E GLY 3.2 4.8 - - - +
22E GLU* 4.8 0.4 - - - -
23E ARG* 2.7 52.2 + - + +
24E VAL 5.1 0.2 - - - -
25E ARG* 4.2 14.6 - - + -
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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