Contacts of the strand formed by residues 37 - 46 (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 LYS 37 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31E GLY* 3.3 0.9 - - - -
32E LYS* 2.8 35.3 + - + +
35E GLU* 3.2 29.1 + - + +
36E GLY* 1.3 83.1 - - - +
38E GLN* 1.3 63.4 + - - +
68E PHE* 3.7 3.3 - - - -
211E GLU 3.3 5.8 - - - +
212E HIS* 3.7 38.6 - - + -
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Residues in contact with GLN 38 (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 24.5 - - + +
30E LEU* 3.5 13.5 - - - +
31E GLY* 3.8 3.4 - - - -
37E LYS* 1.3 76.1 - - - +
39E SER* 1.3 61.8 + - - +
40E MET* 3.9 6.7 - - - +
63E KZ4 3.7 28.2 - - - +
65E ASN* 4.2 5.1 + - - +
68E PHE* 3.6 34.0 - - + +
116E TYR* 4.2 4.0 + - - -
210E HIS* 3.4 6.2 + - - +
211E GLU* 2.8 64.7 + - + +
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Residues in contact with SER 39 (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* 4.5 1.6 - - - +
29E GLY* 3.2 1.2 - - - -
30E LEU* 2.9 51.6 + - - +
38E GLN* 1.3 78.3 - - - +
40E MET* 1.3 64.5 + - - +
208E ASN* 4.9 3.9 + - - -
209E LEU 3.1 7.4 - - - -
210E HIS* 3.4 36.3 + - - -
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Residues in contact with MET 40 (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* 4.1 14.8 - - + -
12E LEU* 3.7 33.2 - - + -
28E VAL 3.4 15.0 - - - +
29E GLY* 3.6 4.7 - - - -
38E GLN* 3.9 21.5 - - - +
39E SER* 1.3 78.0 - - - +
41E ASP* 1.3 64.5 + - - +
42E LEU* 3.8 20.0 - - + -
61E PHE* 3.8 26.9 - - - +
63E KZ4 4.0 6.3 - - - -
116E TYR* 4.5 0.2 - - + -
207E VAL 3.6 0.9 - - - +
208E ASN* 3.3 6.8 + - - +
209E LEU* 2.8 49.5 + - + +
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Residues in contact with ASP 41 (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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26E GLU 4.1 0.3 - - - +
27E GLY* 3.2 2.6 - - - -
28E VAL* 2.7 42.5 + - + +
40E MET* 1.3 72.5 - - - +
42E LEU* 1.3 61.2 + - - +
43E LYS* 4.4 20.0 + - - +
207E VAL 3.3 3.9 - - - +
208E ASN* 3.1 33.2 + - - +
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Residues in contact with LEU 42 (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* 4.0 3.1 - - + -
25E ILE* 4.2 3.4 - - + -
26E GLU 3.5 2.0 - - - +
27E GLY* 3.9 15.5 - - - -
40E MET* 3.8 17.0 - - - -
41E ASP* 1.3 76.3 - - - +
43E LYS* 1.3 64.2 + - - +
54E TYR* 3.4 22.0 - - + +
61E PHE* 3.6 50.0 - - + -
204E TYR 5.4 0.2 - - - +
205E SER 3.5 0.6 - - - +
206E ASN* 3.3 7.3 - - - +
207E VAL* 2.7 43.6 + - + +
209E LEU* 3.8 31.0 - - + -
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Residues in contact with LYS 43 (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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25E ILE* 3.5 4.3 - - - -
26E GLU 2.8 35.2 + - - +
28E VAL* 5.4 6.9 - - - +
41E ASP* 4.4 22.6 + - - +
42E LEU* 1.3 75.8 - - - +
44E VAL* 1.3 65.5 + - - +
45E LYS* 3.4 33.6 + - + +
205E SER 3.3 4.5 - - - +
206E ASN* 3.5 24.5 + - - +
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Residues in contact with VAL 44 (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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24E ALA 3.8 5.8 - - - +
25E ILE* 3.9 11.7 - - + -
42E LEU 6.1 0.2 - - - -
43E LYS* 1.3 72.7 - - - +
45E LYS* 1.3 65.5 + - - +
46E GLU 3.5 21.1 - - - +
48E GLY* 3.9 23.3 - - - +
50E LEU* 3.8 30.3 - - + +
54E TYR* 4.3 3.4 - - + +
203E ASP 5.7 0.2 - - - +
204E TYR 3.7 23.6 - - - +
205E SER* 3.1 20.1 + - - +
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Residues in contact with LYS 45 (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* 4.6 7.6 - - - +
24E ALA 2.8 11.5 + - - +
25E ILE 4.7 0.2 - - - -
26E GLU* 3.5 48.9 - - + +
43E LYS* 3.7 41.4 - - - +
44E VAL* 1.3 77.7 - - - +
46E GLU* 1.3 71.0 + - + +
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Residues in contact with GLU 46 (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* 3.1 25.2 + - - -
15E GLU* 5.0 2.9 - - - +
23E PHE* 3.3 8.9 - - - +
24E ALA* 3.0 44.4 + - + +
44E VAL* 3.5 5.5 - - - +
45E LYS* 1.3 85.2 - - + +
47E GLY* 1.3 63.9 + - - +
48E GLY 3.3 4.9 + - - +
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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