Contacts of the strand formed by residues 84 - 91 (chain D) in PDB entry 2I6A
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 ALA 84 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9D LEU* 3.4 21.5 - - + -
70D ILE* 3.5 33.7 - - + +
73D ALA 5.4 0.2 - - - -
74D GLN* 2.9 18.4 + - + +
77D ILE* 5.6 0.9 - - + -
82D LYS 4.6 0.2 - - - -
83D ALA* 1.3 79.4 - - + +
85D THR* 1.3 63.1 + - - +
108D VAL* 3.4 5.3 - - + +
109D ASP* 2.9 28.7 + - - +
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Residues in contact with THR 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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7D ASN* 2.9 42.9 + - - +
9D LEU 2.7 13.7 + - - +
10D PHE* 4.1 12.8 - - + -
11D GLY* 2.9 27.3 + - - +
70D ILE* 4.1 7.1 - - - +
84D ALA* 1.3 72.3 - - - +
86D PHE* 1.3 66.3 + - - +
87D PHE* 3.7 23.6 - - + -
109D ASP 3.4 14.6 - - - +
111D HIS* 4.1 4.5 - - + -
158D LEU* 4.2 11.5 + - + +
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Residues in contact with PHE 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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11D GLY 3.1 19.1 - - - -
12D MET* 3.7 3.4 - - - -
13D GLY* 3.3 39.5 - - - -
14D ASN 4.6 0.2 - - - -
15D PRO* 3.7 20.6 - - + -
66D THR* 4.1 1.6 - - - -
67D GLN* 3.3 61.5 - - + -
70D ILE* 4.4 9.9 - - + -
85D THR* 1.3 78.5 - - - +
87D PHE* 1.3 66.8 + - - +
108D VAL* 4.1 17.7 - - + -
109D ASP 3.4 4.9 + - - -
110D ALA* 3.4 4.0 - - + -
111D HIS 2.8 30.8 + - - -
112D TYR* 3.8 18.6 - + - -
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Residues in contact with PHE 87 (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 PHE* 3.6 26.7 - + - -
11D GLY 3.1 6.3 + - - -
12D MET* 3.2 33.2 - - + +
13D GLY 3.3 6.6 + - - +
85D THR* 3.7 19.3 - - + -
86D PHE* 1.3 91.5 - - - +
88D GLY* 1.3 57.6 + - - +
111D HIS* 3.0 31.0 - + + +
144D TYR* 3.8 14.4 - - - +
149D HIS* 3.5 18.8 - + + -
150D LEU* 4.4 6.5 - - + -
155D ASN* 3.4 47.3 - - + -
158D LEU* 4.3 10.3 - - + -
159D VAL* 4.0 5.4 - - + -
171D PHE* 5.3 0.2 - - - -
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Residues in contact with GLY 88 (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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13D GLY 3.7 8.1 - - - -
15D PRO* 3.6 20.2 - - - -
87D PHE* 1.3 75.9 - - - +
89D CYS* 1.3 59.1 + - - -
90D ILE 4.1 0.2 - - - -
111D HIS 3.5 4.0 + - - -
112D TYR* 3.1 10.5 - - - +
113D TYR* 2.8 24.3 + - - +
144D TYR* 3.8 15.6 - - - -
171D PHE* 5.7 0.2 - - - -
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Residues in contact with CYS 89 (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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13D GLY 4.7 0.4 + - - -
15D PRO* 3.9 9.0 - - - +
88D GLY* 1.3 73.0 - - - -
90D ILE* 1.3 67.2 + - - +
113D TYR* 3.3 31.9 - - + +
115D GLN* 3.9 10.1 - - - -
120D THR* 5.7 0.2 - - - -
140D ALA 3.1 22.2 - - - +
141D ALA* 3.3 15.6 + - - +
143D CYS* 3.1 31.4 - - - -
144D TYR* 3.7 25.7 - - + +
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Residues in contact with ILE 90 (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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15D PRO* 3.6 33.7 - - + +
88D GLY 4.0 0.2 + - - -
89D CYS* 1.3 72.4 - - - +
91D GLY* 1.3 69.5 + - - +
96D GLY* 3.9 10.1 - - - +
99D LEU* 4.3 15.9 - - + -
100D LYS* 3.5 35.7 - - + -
112D TYR* 4.0 16.2 - - + -
113D TYR 2.9 11.8 + - - +
114D GLU* 3.9 23.6 - - + +
115D GLN* 2.9 26.5 + - - +
120D THR* 3.9 9.2 - - + +
140D ALA* 3.5 9.2 - - - -
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Residues in contact with GLY 91 (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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90D ILE* 1.3 87.8 - - - +
92D ILE* 1.3 63.2 + - - +
93D ASP* 3.3 7.3 + - - +
96D GLY* 3.9 4.9 - - - -
114D GLU* 4.8 0.9 - - - +
115D GLN 3.4 1.6 - - - -
118D GLN 3.2 24.5 - - - -
119D PRO* 4.0 1.3 - - - -
120D THR* 2.9 27.4 + - - -
140D ALA* 3.4 5.5 - - - +
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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