Contacts of the strand formed by residues 51 - 61 (chain D) in PDB entry 2H62
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 51 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46D ARG 3.7 0.2 - - - +
47D ASN* 3.4 1.6 - - - -
48D SER* 3.3 30.5 + - - +
49D SER* 2.9 8.5 + - - -
50D GLY* 1.3 76.5 - - - +
52D ILE* 1.3 63.4 + - - +
53D GLU* 3.5 4.7 + - - +
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Residues in contact with ILE 52 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45D TRP* 3.9 22.7 - - + +
46D ARG 3.4 4.5 - - - -
47D ASN* 3.5 19.3 - - - +
50D GLY 3.6 4.8 + - - +
51D THR* 1.3 71.9 - - - +
53D GLU* 1.3 64.4 + - - +
54D LEU* 4.0 4.1 + - + +
95D PHE* 4.1 27.8 - - + +
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Residues in contact with GLU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ALA* 4.5 7.8 - - - +
45D TRP* 3.2 3.3 - - - -
46D ARG* 2.6 81.4 + - + +
48D SER* 5.9 0.9 - - - +
51D THR 3.5 4.2 + - - +
52D ILE* 1.3 71.5 - - - +
54D LEU* 1.3 79.8 + - - +
55D VAL* 3.3 9.2 + - - +
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Residues in contact with LEU 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D TYR* 3.4 53.9 + - + +
16D ALA* 3.6 12.0 - - - +
44D SER 3.9 12.1 - - - +
45D TRP* 3.8 3.8 - - + -
52D ILE* 3.9 5.7 + - + +
53D GLU* 1.3 79.7 - - - +
55D VAL* 1.3 62.5 + - - +
57D LYS* 3.7 24.5 - - + +
95D PHE* 3.4 36.8 - - + -
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Residues in contact with VAL 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A VAL* 3.7 35.7 - - + -
14D TYR* 3.8 3.2 - - - -
16D ALA* 3.0 34.7 + - + +
17D ASN* 5.8 3.4 - - - +
44D SER* 2.8 19.2 + - - +
45D TRP* 3.6 15.0 - - - +
46D ARG* 3.7 26.7 - - + +
53D GLU* 3.3 20.8 + - - +
54D LEU* 1.3 73.2 - - - +
56D LYS* 1.3 74.7 + - + +
81D VAL* 5.1 1.3 - - + -
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Residues in contact with LYS 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LEU* 4.5 1.6 - - + -
97A LYS* 5.9 0.4 - - - +
98A VAL* 3.4 34.7 + - + +
99A VAL* 4.7 0.2 - - - +
100A LEU* 4.4 20.2 - - + +
14D TYR* 3.3 13.7 - - - +
15D ASN* 3.1 25.7 + - + +
17D ASN* 4.5 9.1 + - - +
21D GLU* 3.4 21.7 + - - -
42D TYR* 3.5 22.6 - - + +
43D ALA* 3.3 1.9 - - - -
44D SER* 2.8 41.8 + - - +
54D LEU* 4.8 0.4 - - - +
55D VAL* 1.3 98.2 + - + +
57D LYS* 1.3 64.5 + - - +
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Residues in contact with LYS 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ILE* 3.4 27.4 - - + +
13D TYR* 3.4 8.3 - - - -
14D TYR* 2.9 44.6 + - + +
42D TYR* 3.2 12.8 + - - +
43D ALA* 3.9 10.8 - - + -
54D LEU* 3.7 16.6 - - + +
56D LYS* 1.3 77.9 - - - +
58D GLY* 1.3 59.3 + - - +
92D ASN* 3.0 20.3 + - - +
93D GLU* 2.8 35.6 + - - +
95D PHE* 3.7 28.5 - - - -
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Residues in contact with GLY 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LEU* 5.9 1.1 - - - -
11D CYS* 3.8 7.2 - - - -
12D ILE 3.2 12.6 + - - -
13D TYR* 4.5 1.6 - - - -
29D GLU* 3.4 11.7 - - - -
41D CYS* 3.2 4.3 - - - -
42D TYR* 2.9 42.1 + - - -
57D LYS* 1.3 74.6 - - - +
59D CYS* 1.3 62.3 + - - -
92D ASN* 3.7 1.7 + - - -
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Residues in contact with CYS 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A SER* 4.8 1.2 + - - -
100A LEU* 4.6 8.2 - - - +
102A ASN* 5.4 1.4 + - - +
11D CYS* 3.8 3.1 - - - -
29D GLU* 2.9 43.1 + - - +
31D CYS* 2.0 59.7 - - + -
40D HIS 3.5 6.3 - - - -
42D TYR* 3.4 13.0 - - - -
58D GLY* 1.3 75.2 - - - -
60D TRP* 1.3 59.6 + - - +
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Residues in contact with TRP 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ALA* 3.8 26.0 - - + -
35A PRO 4.3 0.4 - - - -
88A SER* 3.4 44.7 + - - +
89A MET 4.2 0.4 - - - -
90A LEU* 3.8 13.0 - - + -
100A LEU* 3.9 17.9 - - + -
31D CYS* 6.1 0.3 - - - +
39D LEU* 4.5 1.0 - - - -
40D HIS* 2.9 42.6 + - + +
41D CYS 4.2 0.7 - - - -
42D TYR* 3.7 34.8 - + + -
59D CYS* 1.3 76.4 - - - +
61D LEU* 1.3 82.1 + - - +
63D ASP* 3.0 27.5 + - - +
66D CYS* 3.6 23.6 - - - -
83D PHE* 3.6 32.5 - + - -
85D CYS* 4.6 0.2 - - + -
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Residues in contact with LEU 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ALA* 3.7 41.1 - - + +
87A ILE* 3.9 8.3 - - - +
88A SER* 2.8 23.4 + - - +
102A ASN* 3.9 29.2 - - + +
32D GLU 4.0 20.6 - - - +
33D GLY* 5.0 7.0 - - - -
34D GLU* 5.7 4.9 - - + +
38D ARG 5.0 0.9 - - - -
39D LEU* 5.7 0.4 - - - +
40D HIS* 3.4 1.4 - - - -
60D TRP* 1.3 90.1 + - - +
62D ASP* 1.3 71.1 + - - +
63D ASP* 3.1 3.8 + - - +
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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