Contacts of the strand formed by residues 79 - 85 (chain D) in PDB entry 5IRC
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 VAL 79 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D LYS 3.2 2.6 + - - +
8D LEU* 3.8 29.2 - - + +
9D VAL 3.1 23.7 + - - -
55D LEU* 4.9 3.1 - - + -
77D THR* 3.3 4.7 - - - +
78D ASP* 1.3 79.6 - - - +
80D ILE* 1.3 73.6 + - - +
81D LEU* 5.0 0.2 - - + -
110D VAL* 3.6 4.7 - - - -
111D PRO* 3.8 9.9 - - + +
113D ILE* 4.1 6.1 - - + -
174D ALA* 3.6 38.8 - - + +
177D ALA* 4.1 11.2 - - + -
178D ALA* 3.8 14.1 - - + +
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Residues in contact with ILE 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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9D VAL* 3.3 10.3 - - + +
11D VAL* 4.2 13.7 - - + -
74D TYR* 4.4 17.0 - - + -
77D THR* 3.9 8.7 - - + -
79D VAL* 1.3 77.8 - - - +
81D LEU* 1.3 78.8 - - - +
82D MET* 3.9 8.3 - - + +
103D VAL* 3.5 36.3 - - + -
107D CYS* 4.3 17.5 - - + -
110D VAL* 3.8 13.7 - - + -
111D PRO 3.1 12.1 + - - +
112D ILE* 4.4 7.4 - - + -
113D ILE* 2.9 27.5 + - - +
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Residues in contact with LEU 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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8D LEU* 3.8 30.3 - - + -
9D VAL 2.9 6.9 + - - +
10D ILE* 3.3 19.4 - - + +
11D VAL 2.9 28.2 + - - +
21D LEU* 4.1 16.8 - - + -
79D VAL 4.3 0.4 + - - -
80D ILE* 1.3 74.6 - - - +
82D MET* 1.3 61.4 + - - +
83D CYS* 3.9 5.6 - - - -
113D ILE* 3.6 26.9 - - + -
115D VAL* 4.2 3.6 - - + -
170D VAL* 4.1 13.7 - - + -
171D PHE* 3.9 22.7 - - + -
174D ALA* 3.8 22.7 - - + -
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Residues in contact with MET 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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11D VAL* 3.6 11.9 - - + +
80D ILE* 3.8 3.0 - - + -
81D LEU* 1.3 72.4 - - - +
83D CYS* 1.3 60.0 + - - +
95D ILE* 3.6 31.2 - - + -
99D TRP* 3.7 35.0 - - + +
100D THR* 3.7 26.7 - - - +
103D VAL* 3.8 19.5 - - + -
112D ILE* 3.8 31.4 - - + -
113D ILE 2.9 7.5 + - - -
114D LEU* 3.4 9.1 - - + +
115D VAL 2.9 24.9 + - - -
151D ILE* 4.0 9.4 - - + -
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Residues in contact with CYS 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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10D ILE* 3.6 37.0 - - - -
11D VAL 2.8 13.6 + - - +
12D GLY* 3.4 18.9 - - - -
13D ASP 4.1 1.6 + - - -
16D CYS* 3.8 11.6 - - - -
18D LYS* 4.3 2.2 - - + -
21D LEU* 4.3 4.0 - - - -
81D LEU* 4.2 3.6 - - - -
82D MET* 1.3 78.1 - - - +
84D PHE* 1.3 63.4 - - - +
91D SER* 5.0 0.9 - - - +
95D ILE* 3.7 9.8 - - - +
99D TRP* 4.9 0.7 - - - -
115D VAL* 3.3 20.6 - - - +
117D ASN* 3.6 25.1 - - - +
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Residues in contact with PHE 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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16D CYS* 4.1 8.3 - - - -
83D CYS* 1.3 72.7 - - - +
85D SER* 1.3 70.4 + - - +
86D ILE* 4.1 8.3 - - + -
91D SER* 3.2 33.7 - - - +
92D LEU* 3.9 30.5 - - + -
95D ILE* 4.2 2.9 - - + -
114D LEU* 4.0 19.7 - - + -
115D VAL 3.0 14.1 + - - +
116D GLY* 3.6 19.5 - - - -
117D ASN* 2.8 29.1 + - - +
139D VAL* 3.9 23.8 - - + -
144D GLY* 4.4 4.3 - - - -
156D TYR* 3.5 36.1 - + - -
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Residues in contact with SER 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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16D CYS* 3.8 26.4 - - - +
84D PHE* 1.3 82.3 - - - +
86D ILE* 1.3 60.0 + - - +
87D ASP* 2.3 30.4 + - - -
88D SER* 2.9 30.2 + - - +
91D SER* 2.9 14.3 + - - -
117D ASN 3.7 3.6 - - - -
118D LYS* 3.2 17.6 - - - +
139D VAL* 4.1 0.3 - - - +
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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