Contacts of the strand formed by residues 40 - 48 (chain E) in PDB entry 1HNX
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 ARG 40 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E PHE* 3.7 26.2 - - + -
35E GLY* 3.1 22.7 - - - -
36E ASP* 3.0 31.5 + - - +
38E GLN 3.1 5.4 - - - +
39E GLY* 1.3 77.9 - - - +
41E VAL* 1.3 60.7 + - - +
66E MET* 3.8 31.0 - - + +
67E VAL 3.4 4.3 - - - -
68E GLU* 2.6 60.5 + - - +
112E LEU 3.6 1.2 - - - +
113E ALA 3.9 2.0 + - - -
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Residues in contact with VAL 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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33E VAL* 3.9 16.2 - - + -
34E VAL 3.2 13.9 - - - +
40E ARG* 1.3 72.8 - - - +
42E GLY* 1.3 57.2 + - - +
66E MET* 3.1 5.6 - - - +
67E VAL* 2.5 42.2 + - + +
69E VAL* 3.6 17.5 - - + -
109E ILE* 3.7 25.4 - - + +
112E LEU 3.9 5.4 - - - +
113E ALA* 3.2 39.7 - - + +
136E MET* 3.9 9.1 - - + +
139E LEU* 4.4 6.5 - - + -
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Residues in contact with GLY 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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32E VAL 3.6 1.0 - - - +
33E VAL* 3.5 5.0 - - - +
34E VAL* 2.7 41.8 + - - -
41E VAL* 1.3 77.1 - - - +
43E LEU* 1.3 60.3 + - - -
62E ALA* 3.5 16.9 - - - +
65E ASN 3.3 16.4 - - - -
66E MET* 3.8 5.1 - - - -
136E MET* 3.7 3.6 - - - -
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Residues in contact with LEU 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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31E LEU* 3.1 37.2 - - + -
32E VAL 3.2 9.0 - - - +
33E VAL* 4.5 11.2 - - + +
42E GLY* 1.3 73.0 - - - -
44E GLY* 1.3 78.9 + - - +
61E TYR 4.1 1.4 - - - +
62E ALA* 3.6 6.4 - - - -
65E ASN* 3.0 22.8 + - - +
109E ILE* 4.2 6.7 - - + -
132E ALA* 3.3 33.4 - - + +
133E TYR* 3.9 18.5 - - + -
136E MET* 3.3 41.3 - - + +
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Residues in contact with GLY 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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30E ALA 3.3 2.3 - - - +
31E LEU* 3.3 4.1 - - - +
32E VAL* 2.6 44.9 + - - +
43E LEU* 1.3 77.3 - - - +
45E PHE* 1.3 61.2 + - - -
46E GLY 3.9 0.7 - - - -
58E ALA* 3.6 8.5 - - - +
61E TYR* 4.2 4.3 - - - -
62E ALA* 3.2 21.2 - - - +
133E TYR* 5.7 0.7 - - - -
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Residues in contact with PHE 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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1079A G 4.0 16.8 - - - -
1080A A 3.8 8.3 - - - -
12E LEU* 4.8 3.1 - - + -
14E ARG* 3.9 17.3 - - - -
29E GLY* 4.0 12.3 - - - -
30E ALA 3.1 29.8 - - - -
31E LEU* 3.5 24.0 - - + -
44E GLY* 1.3 72.7 - - - -
46E GLY* 1.3 56.7 + - - +
47E LYS* 3.4 46.6 + - + +
61E TYR* 4.0 14.4 - - - +
129E ILE* 3.3 33.7 - - + -
133E TYR* 3.6 20.1 + - - +
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Residues in contact with GLY 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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28E PHE 3.7 1.2 - - - +
30E ALA* 2.9 37.0 + - - +
45E PHE* 1.3 74.8 - - - +
47E LYS* 1.3 63.3 + - - -
54E ALA* 3.6 8.5 - - - +
57E LYS* 4.4 1.6 - - - -
58E ALA* 3.9 15.7 - - - +
61E TYR* 4.0 19.7 - - - -
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Residues in contact with LYS 47 (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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1077A G 2.7 29.3 + - - -
1079A G 4.1 6.8 + - - -
1080A A 3.7 27.6 - - - +
1081A G 4.9 5.3 + - - +
27E ARG* 4.5 15.9 - - + -
28E PHE 3.0 12.3 - - - +
29E GLY* 4.6 2.5 - - - -
45E PHE* 3.4 43.4 + - + +
46E GLY* 1.3 78.5 - - - -
48E ALA* 1.3 63.2 + - - +
54E ALA* 4.6 0.2 - - - -
57E LYS* 2.8 27.7 + - - +
61E TYR* 5.3 1.3 - - + -
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Residues in contact with ALA 48 (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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1072A G 4.5 0.9 - - - +
27E ARG* 4.3 5.5 - - - +
28E PHE* 2.9 33.6 + - - +
46E GLY 4.3 0.2 + - - -
47E LYS* 1.3 80.3 - - - +
49E PRO* 1.3 77.5 - - + +
50E GLU 3.1 2.0 + - - +
53E LEU* 3.9 13.0 - - + -
54E ALA* 3.7 25.0 - - - +
57E LYS* 3.5 13.0 - - - +
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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