Contacts of the strand formed by residues 92 - 98 (chain A) in PDB entry 1I6P
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 HIS 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ARG* 3.2 17.4 + - - +
37A PHE* 3.3 39.6 - + + -
38A LEU* 2.9 24.4 + - - +
90A VAL* 3.6 2.2 - - - +
91A GLU* 1.3 97.7 + - + +
93A ILE* 1.3 66.1 + - - +
94A ILE* 5.0 1.8 - - + -
175A THR* 3.3 19.2 - - - -
177A HIS* 2.9 34.8 + + + +
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Residues in contact with ILE 93 (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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38A LEU* 3.4 35.7 - - + +
40A ILE* 4.3 8.5 - - + -
81A VAL* 4.5 1.6 - - + -
85A VAL* 3.9 28.0 - - + -
90A VAL* 4.2 6.7 - - + -
92A HIS* 1.3 77.4 - - - +
94A ILE* 1.3 66.1 + - - +
95A ILE* 4.8 1.1 - - + -
158A LEU* 3.6 30.5 - - + -
164A MET* 4.0 14.8 - - + -
174A VAL* 3.9 14.8 - - + -
175A THR 2.7 11.8 + - - +
176A ILE* 3.3 7.7 - - + +
177A HIS* 2.8 28.8 + - - +
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Residues in contact with ILE 94 (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 PHE* 4.3 25.6 - - + -
38A LEU 2.8 13.4 + - - +
39A TRP* 3.5 27.6 - - + -
40A ILE* 2.8 28.8 + - - +
53A THR* 5.9 0.9 - - + -
55A LEU* 6.1 2.5 - - + -
92A HIS 5.0 2.5 - - - -
93A ILE* 1.3 80.7 - - - +
95A ILE* 1.3 71.9 + - - +
96A CYS* 3.8 3.8 + - + -
177A HIS* 3.8 19.5 - - + +
179A TRP* 3.6 54.1 - - + -
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Residues in contact with ILE 95 (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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40A ILE* 3.4 25.4 - - + +
68A ASN* 4.2 21.1 - - + +
70A VAL* 3.8 16.4 - - + -
93A ILE* 4.8 2.0 - - + -
94A ILE* 1.3 73.9 - - - +
96A CYS* 1.3 60.5 + - - +
151A VAL* 3.7 15.4 - - + +
154A GLN* 3.6 42.0 - - + +
155A VAL* 3.7 14.1 - - + +
158A LEU* 4.2 15.3 - - + -
176A ILE* 4.8 1.6 - - + -
177A HIS 3.0 13.8 + - - +
178A GLY* 3.7 1.4 - - - -
179A TRP 3.0 24.9 + - - +
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Residues in contact with CYS 96 (chain A).
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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39A TRP* 3.4 41.0 + - + +
40A ILE 3.0 10.1 + - - -
41A GLY* 3.7 18.5 - - - -
42A CYS* 4.1 2.6 + - - +
68A ASN* 3.8 9.4 - - - +
94A ILE* 3.8 5.8 + - + -
95A ILE* 1.3 74.5 - - - +
97A GLY* 1.3 72.1 + - - +
98A HIS* 5.5 0.2 - - - -
179A TRP* 3.4 13.5 - - + -
180A ALA 4.2 0.2 - - - -
181A TYR* 3.6 21.5 - - - -
188A LEU* 4.1 15.5 - - - -
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Residues in contact with GLY 97 (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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68A ASN* 3.6 16.2 - - - -
96A CYS* 1.3 81.3 - - - +
98A HIS* 1.3 63.8 + - - +
147A CYS* 4.5 3.1 - - - -
151A VAL* 3.6 19.3 - - - +
179A TRP 3.0 10.5 + - - -
180A ALA* 3.2 22.6 - - - -
181A TYR* 3.3 4.4 + - - -
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Residues in contact with HIS 98 (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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42A CYS* 4.0 13.5 - - + -
44A ASP* 3.3 9.3 + - + +
45A SER 5.7 0.7 - - - -
46A ARG* 3.4 31.8 - - + +
68A ASN* 4.8 0.6 + - - -
96A CYS 5.5 0.2 - - - -
97A GLY* 1.3 77.7 - - - +
99A TYR* 1.3 71.8 + - - +
100A GLY 4.5 2.2 - - - -
101A CYS* 3.3 32.4 + - + +
147A CYS* 3.1 18.6 - - - -
180A ALA* 5.0 0.4 - - - +
181A TYR* 3.2 40.1 - + + +
182A GLY* 5.6 0.2 - - - -
183A ILE* 5.1 1.8 - - + +
301A ZN 2.2 35.8 - - - -
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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