Contacts of the strand formed by residues 48 - 58 (chain A) in PDB entry 2HR6
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 THR 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A LEU* 3.9 3.5 - - - +
46A GLY 4.6 1.2 + - - -
47A ASP* 1.3 76.6 - - - +
49A THR* 1.3 68.2 + - - +
83A GLY* 4.5 6.6 - - - -
100A SER* 3.5 24.9 - - - +
101A VAL 3.2 11.2 - - - +
102A TRP* 3.7 17.5 - - - +
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Residues in contact with THR 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A VAL* 4.0 19.0 - - + +
43A LEU* 3.9 15.7 - - + +
48A THR* 1.3 79.2 - - - +
50A LEU* 1.3 65.6 + - - +
51A VAL* 3.7 11.0 + - + +
99A ILE 3.6 0.3 - - - +
100A SER* 3.8 1.4 - - - -
101A VAL* 2.9 35.8 + - + +
111A ILE* 3.6 31.2 - - + -
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 5.4 1.2 - - - +
49A THR* 1.3 78.8 + - - +
51A VAL* 1.3 60.3 + - - +
52A PRO* 3.8 7.1 - - - +
98A MET* 3.7 42.5 - - + +
99A ILE 3.6 16.2 - - - +
100A SER* 4.4 9.2 - - - +
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Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ALA* 3.7 29.2 - - + -
36A CYS 4.5 0.4 - - - +
37A LEU* 4.5 9.6 - - + -
41A VAL* 6.0 1.3 - - + -
49A THR* 3.9 17.3 - - + +
50A LEU* 1.3 76.3 - - - +
52A PRO* 1.4 78.8 - - + +
98A MET* 3.7 4.3 - - - -
99A ILE* 2.8 52.9 + - + +
101A VAL* 3.7 24.7 - - + -
111A ILE* 4.4 13.0 - - + -
117A ILE* 4.9 2.5 - - + -
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Residues in contact with PRO 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ARG 4.0 0.2 - - - +
35A ALA* 3.9 1.0 - - - -
36A CYS* 2.9 44.8 + - + +
37A LEU* 3.9 15.3 - - + -
50A LEU 3.8 7.2 - - - +
51A VAL* 1.4 90.9 - - - +
53A THR* 1.3 60.8 + - - +
54A GLY 4.3 2.0 - - - +
96A GLN* 3.3 22.0 - - - +
98A MET* 3.9 18.3 - - + -
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Residues in contact with THR 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 3.5 14.7 - - - +
33A LEU* 4.7 15.5 - - + -
34A ARG 3.8 14.9 - - - +
36A CYS* 3.5 7.9 - - - +
52A PRO* 1.3 72.2 - - - +
54A GLY* 1.3 63.1 + - - +
55A LEU* 3.2 34.6 + - - +
96A GLN* 3.6 0.4 + - - -
97A LEU* 2.7 37.5 + - + +
99A ILE* 3.9 31.2 - - + -
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Residues in contact with GLY 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ILE* 3.9 1.2 - - - -
10A LEU* 2.9 30.1 + - - -
11A ASP* 3.3 12.9 + - - -
14A VAL* 3.8 8.7 - - - +
36A CYS* 3.7 18.9 - - - +
52A PRO 3.6 1.6 - - - -
53A THR* 1.3 76.8 - - - +
55A LEU* 1.3 61.1 + - - +
96A GLN* 2.9 16.7 + - - -
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Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A VAL* 4.2 9.6 - - + -
8A LYS 3.5 11.7 - - - +
9A ILE* 4.7 1.1 - - - -
10A LEU* 4.0 5.4 - - - -
14A VAL* 4.1 20.6 - - + -
20A LEU* 4.3 5.4 - - + -
21A PRO* 3.9 32.5 - - + -
33A LEU* 6.0 1.6 - - + -
53A THR* 3.2 21.6 + - - +
54A GLY* 1.3 81.6 - - - +
56A ALA* 1.3 57.5 + - - +
57A ILE* 3.9 15.5 - - + -
96A GLN* 3.5 4.5 + - - +
97A LEU* 2.9 55.5 + - + -
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A VAL* 3.3 7.1 - - - +
8A LYS* 2.9 45.8 + - + +
10A LEU* 4.1 13.4 - - + +
55A LEU* 1.3 74.9 - - - +
57A ILE* 1.3 64.8 + - - +
94A GLN 3.7 15.0 - - - +
95A GLY 3.3 23.8 - - - +
97A LEU 4.4 0.9 - - - +
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Residues in contact with ILE 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ILE* 4.2 9.0 - - + -
6A ASP 3.5 9.0 - - - +
7A VAL* 4.3 9.6 - - + -
55A LEU* 3.9 18.4 - - + -
56A ALA* 1.3 79.5 - - - +
58A HIS* 1.3 62.1 + - - +
59A ILE* 3.9 28.0 - - + -
66A ALA* 5.1 0.4 - - + -
89A ILE* 4.6 7.9 - - + -
93A TYR* 2.9 20.7 - - + +
94A GLN* 3.8 7.8 - - - -
95A GLY 4.4 2.6 + - - +
97A LEU* 4.1 30.4 - - + +
120A MET* 4.3 7.2 - - + -
122A PHE* 3.9 23.1 - - + -
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Residues in contact with HIS 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ILE* 4.0 9.9 - - - +
6A ASP* 3.1 35.4 + - + +
57A ILE* 1.3 75.1 - - - +
59A ILE* 1.3 67.2 + - - +
60A ALA* 3.5 30.8 - - + +
91A SER 3.3 19.8 + - - -
92A ASP* 4.4 7.5 - - - +
93A TYR 4.0 2.9 - - - -
94A GLN* 3.2 41.6 + - + +
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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