Contacts of the strand formed by residues 79 - 86 (chain D) in PDB entry 2PQA
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 ILE 79 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ILE* 4.9 0.2 - - + -
17D LEU* 3.8 26.7 - - + -
25D VAL* 3.8 16.8 - - + -
27D PHE* 3.7 33.2 - - + -
51D GLY* 6.2 0.7 - - - -
52D THR 3.0 5.4 + - - +
53D ILE* 3.4 20.3 - - + +
54D GLU* 2.7 32.2 + - - +
69D VAL* 3.9 18.2 - - + -
71D GLY* 3.8 31.9 - - - +
72D ARG 3.4 3.1 - - - +
73D VAL* 4.3 2.2 - - + -
78D THR* 1.3 80.2 - - - +
80D LEU* 1.3 59.7 + - - +
81D CYS 3.6 0.3 + - - -
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Residues in contact with LEU 80 (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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4D MET* 5.3 0.2 - - - +
54D GLU* 3.4 29.2 - - + +
55D LEU* 4.4 0.4 - - - -
56D MET* 3.8 41.7 - - + +
71D GLY* 3.0 22.0 - - - -
72D ARG* 2.9 21.1 + - + +
74D THR* 4.0 18.9 - - + +
79D ILE* 1.3 70.5 - - - +
81D CYS* 1.3 64.3 + - - +
82D THR* 4.9 6.2 + - + +
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Residues in contact with CYS 81 (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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41D PHE* 5.2 1.1 - - - -
53D ILE* 3.7 17.9 - - + -
54D GLU 2.7 19.1 + - - +
55D LEU* 3.6 32.9 - - + +
56D MET* 5.0 3.1 + - - +
69D VAL* 4.2 12.3 - - + -
70D VAL 3.4 7.0 - - - +
71D GLY* 4.2 0.7 - - - -
79D ILE* 3.6 1.9 + - - -
80D LEU* 1.3 77.7 - - - +
82D THR* 1.3 61.3 + - - +
83D SER* 3.3 32.5 - - - -
84D TYR* 4.3 12.6 - - - -
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Residues in contact with THR 82 (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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4D MET* 4.0 28.7 - - + +
5D MET* 5.2 4.6 - - - -
55D LEU* 5.8 1.1 - - - -
70D VAL* 2.8 15.4 + - - +
71D GLY* 3.9 8.1 - - - -
80D LEU* 3.9 7.3 + - + +
81D CYS* 1.3 76.8 - - - +
83D SER* 1.3 64.2 + - - +
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Residues in contact with SER 83 (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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81C ARG* 4.9 5.3 + - - -
5D MET* 3.8 25.5 - - - +
70D VAL* 2.7 57.1 + - - +
81D CYS* 3.3 10.4 - - - -
82D THR* 1.3 82.1 - - - +
84D TYR* 1.3 60.0 + - - +
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Residues in contact with TYR 84 (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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123C GLU* 5.2 0.9 - - - +
41D PHE* 5.4 2.9 - + - -
55D LEU* 5.3 7.2 - - + -
59D LEU* 3.7 22.1 - - + +
60D ASP* 5.1 2.6 + - - -
61D GLU* 2.6 31.5 + - - +
63D ILE* 3.5 27.0 - - + +
67D VAL* 3.9 24.0 - - + -
68D GLU 2.9 13.5 - - - +
69D VAL* 4.0 11.7 - - + -
70D VAL* 5.7 0.4 - - - -
81D CYS* 4.3 10.3 - - - -
83D SER* 1.3 83.2 - - - +
85D VAL* 1.3 74.5 + - - +
86D GLN* 4.3 5.8 - - + -
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Residues in contact with VAL 85 (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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79C ILE* 3.8 14.8 - - + -
81C ARG* 4.9 6.7 - - - +
123C GLU* 3.5 37.9 - - + +
125C TYR* 4.8 5.6 - - + -
67D VAL* 3.4 0.7 - - - -
68D GLU* 2.6 57.5 + - + +
83D SER* 6.4 0.4 - - - -
84D TYR* 1.3 83.2 - - - +
86D GLN* 1.3 75.6 + - - +
87D PHE* 3.6 11.3 + - + -
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Residues in contact with GLN 86 (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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61D GLU* 4.1 9.2 - - - +
62D GLU 3.8 7.4 + - - +
63D ILE* 3.5 26.2 - - + +
64D SER* 2.8 53.8 + - - +
66D ILE 3.7 7.2 - - - +
67D VAL* 4.2 8.5 - - + +
84D TYR* 4.3 7.8 - - + -
85D VAL* 1.3 80.5 - - - +
87D PHE* 1.3 65.9 + - - +
88D LYS* 3.4 7.4 + - - +
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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