Contacts of the strand formed by residues 21 - 32 (chain E) in PDB entry 6NQN
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 21 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17E ALA* 3.3 16.1 - - - -
18E VAL 3.3 16.4 + - - +
19E ASN* 3.7 23.1 + - + -
20E GLY* 1.3 74.9 + - - +
22E PRO* 1.3 72.1 - - + +
23E PHE* 3.9 3.6 + - - -
51E PRO* 5.2 19.5 - - + -
52E PHE* 5.6 2.1 - - + -
132E MET* 5.9 4.3 - - + -
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Residues in contact with PRO 22 (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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117B GLU* 6.1 1.3 - - - +
16E GLY 3.4 9.9 - - - +
17E ALA* 4.1 5.2 - - + -
20E GLY 3.7 8.9 - - - +
21E HIS* 1.3 88.3 - - + +
23E PHE* 1.3 62.1 + - - +
46E GLU* 5.6 0.6 - - - +
47E GLY* 3.5 16.8 + - - +
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Residues in contact with PHE 23 (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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14E MET* 3.5 31.2 - - + -
15E GLU* 3.8 1.2 - - - +
16E GLY* 2.8 39.3 + - - +
17E ALA* 3.4 30.7 - - - -
18E VAL* 4.0 3.4 - - + -
21E HIS 4.1 2.5 - - - -
22E PRO* 1.3 76.9 - - - +
24E ALA* 1.3 65.8 + - - +
25E ILE* 3.8 23.8 - - + -
46E GLU* 3.3 20.6 - - - +
47E GLY* 4.2 2.2 - - - +
50E LEU* 3.8 20.0 - - + -
52E PHE* 3.7 20.9 - + + -
57E LEU* 3.6 23.8 - - + -
120E PHE* 4.0 7.0 - + - -
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Residues in contact with ALA 24 (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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13E ARG* 3.7 30.1 - - - +
14E MET 3.2 11.9 - - - +
15E GLU* 4.6 4.5 - - - +
23E PHE* 1.3 79.5 - - - +
25E ILE* 1.3 65.7 + - - +
44E VAL* 3.7 0.3 - - - -
45E LYS* 2.8 26.0 + - + -
46E GLU* 3.0 29.8 + - + +
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Residues in contact with ILE 25 (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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12E LEU* 4.3 0.9 - - - +
13E ARG* 3.4 2.6 - - - +
14E MET* 2.7 40.2 + - + +
23E PHE* 3.8 17.7 - - + -
24E ALA* 1.3 79.9 - - - +
26E GLU* 1.3 74.6 + - - +
42E LEU* 4.2 4.5 - - + -
43E LYS 3.5 13.0 - - - +
44E VAL* 3.9 14.6 - - + -
45E LYS* 4.3 0.7 - - - +
50E LEU* 4.1 10.5 - - + -
54E TYR* 3.9 16.6 - - - +
57E LEU* 3.6 31.6 - - + -
61E PHE* 3.5 29.8 - - + -
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Residues in contact with GLU 26 (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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11E LYS* 5.4 8.1 + - - +
12E LEU* 3.4 12.3 - - - +
13E ARG* 2.9 45.2 + - + +
25E ILE* 1.3 81.5 - - - +
27E GLY* 1.3 60.2 + - - +
41E ASP 4.1 0.2 - - - +
42E LEU* 3.5 1.9 - - - -
43E LYS* 2.8 33.7 + - - +
45E LYS* 3.5 31.0 - - + +
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Residues in contact with GLY 27 (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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11E LYS* 3.5 2.0 - - - +
12E LEU* 3.0 48.4 + - - +
26E GLU* 1.3 76.1 - - - +
28E VAL* 1.3 71.0 + - - +
40E MET* 5.5 0.4 - - - -
41E ASP 3.2 11.2 - - - -
42E LEU* 3.9 9.0 - - - -
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Residues in contact with VAL 28 (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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10E ILE* 3.3 10.3 - - - +
11E LYS* 4.6 15.9 - - + +
27E GLY* 1.3 79.0 - - - +
29E GLY* 1.3 59.1 + - - +
40E MET* 4.0 3.6 - - - -
41E ASP* 2.7 40.2 + - + +
43E LYS* 5.4 6.1 - - - +
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Residues in contact with GLY 29 (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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9E LYS* 3.4 7.4 - - - +
10E ILE* 2.6 42.6 + - - +
28E VAL* 1.3 77.3 - - - +
30E LEU* 1.3 60.2 + - - +
39E SER 3.2 13.9 - - - -
40E MET* 3.6 6.5 - - - -
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Residues in contact with LEU 30 (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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8E MET 3.3 11.4 - - - +
9E LYS* 4.1 8.1 - - + +
10E ILE* 4.1 5.5 - - - +
29E GLY* 1.3 75.0 - - - +
31E GLY* 1.3 66.4 + - - +
32E LYS* 5.1 11.9 - - - +
38E GLN* 3.5 3.6 - - - +
39E SER* 2.9 47.3 + - - +
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Residues in contact with GLY 31 (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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7E ASP* 3.8 1.4 - - - +
8E MET* 2.9 32.8 + - - +
30E LEU* 1.3 83.7 - - - +
32E LYS* 1.3 68.0 + - - +
33E PRO* 3.8 0.9 - - - +
37E LYS 3.3 12.6 - - - -
38E GLN* 3.8 2.2 - - - -
68E PHE* 3.5 17.2 - - - -
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Residues in contact with LYS 32 (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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6E PRO 3.4 8.1 - - - +
7E ASP* 3.4 26.9 + - - +
30E LEU* 5.1 12.3 - - - +
31E GLY* 1.3 74.8 - - - -
33E PRO* 1.3 63.6 - - - +
34E PHE 3.2 2.0 - - - +
35E GLU* 2.7 59.1 + - + +
36E GLY 3.0 8.8 + - - -
37E LYS* 2.8 19.1 + - + +
68E PHE* 3.8 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