Contacts of the strand formed by residues 98 - 105 (chain V) in PDB entry 1IR1
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 PHE 98 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12V TYR* 3.5 39.7 - + - -
44V PHE* 3.2 6.6 - - - -
45V GLU 2.9 36.6 + - - +
46V THR* 5.7 5.2 - - - -
49V GLY* 3.9 25.8 - - - -
50V PHE* 4.5 6.5 - + - -
67V TRP* 3.5 25.4 - + + -
96V ASN 5.4 1.1 - - - -
97V ALA* 1.3 74.5 - - - +
99V ILE* 1.3 60.0 + - - +
116V ILE* 5.1 2.5 - - + -
118V TYR 3.5 3.8 - - - +
119V LYS* 4.3 9.6 - - + -
120V PRO* 3.6 24.0 - - + -
123V TYR* 3.8 39.9 - + + -
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Residues in contact with ILE 99 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42V LEU* 4.5 9.9 - - + -
43V GLU 3.4 10.3 - - - +
44V PHE* 4.3 4.0 - - + -
67V TRP* 4.5 1.1 - - - -
87V LEU* 3.8 18.4 - - + -
90V CYS* 3.7 34.5 - - + +
91V LYS* 3.6 37.5 - - + +
94V TYR 4.4 4.3 - - - +
97V ALA* 4.1 4.3 - - + +
98V PHE* 1.3 80.6 - - - +
100V ARG* 1.3 69.7 + - - +
116V ILE* 3.7 2.5 - - - -
117V ALA* 2.8 24.0 + - - -
118V TYR* 2.9 33.3 + - + +
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Residues in contact with ARG 100 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A LYS* 5.6 2.6 - - - +
187A ARG* 5.8 0.4 - - - +
163D ASN* 4.0 21.8 + - - +
41V CYS 4.0 0.2 - - - +
42V LEU* 3.5 6.2 - - - +
43V GLU* 2.8 63.8 + - + +
65V ARG 3.2 23.8 + - - -
66V TYR* 4.9 0.2 - - - +
67V TRP* 3.4 54.3 - - + +
99V ILE* 1.3 76.0 - - - +
101V ILE* 1.3 63.6 + - - +
102V ILE* 4.2 7.6 - - + +
111V GLN* 6.3 0.4 - - - -
114V SER* 4.2 15.2 + - - -
115V PHE 3.2 16.4 - - - +
116V ILE* 3.9 18.6 - - + +
117V ALA 4.1 0.4 - - - +
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Residues in contact with ILE 101 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26V LEU* 4.4 7.4 - - + -
30V VAL* 4.4 14.4 - - + -
33V LEU* 4.2 16.4 - - + -
40V PRO* 5.2 0.4 - - + -
41V CYS 3.7 7.6 - - - +
42V LEU* 4.3 15.3 - - + -
83V VAL* 4.6 20.6 - - + -
84V LEU* 5.3 1.6 - - + -
87V LEU* 4.5 14.4 - - + -
100V ARG* 1.3 76.6 - - - +
102V ILE* 1.3 69.3 + - - +
113V VAL* 4.2 0.7 - - - +
114V SER* 3.2 4.9 + - - -
115V PHE* 2.9 57.5 + - + -
117V ALA* 3.8 24.9 - - + -
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Residues in contact with ILE 102 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A ARG* 4.0 5.6 - - - +
33V LEU* 3.8 7.2 - - - +
39V VAL 3.7 0.2 - - - +
40V PRO* 3.4 4.3 - - - +
41V CYS* 2.9 50.6 + - + +
43V GLU* 3.7 37.7 - - + +
100V ARG* 4.2 9.6 - - + +
101V ILE* 1.3 81.1 - - - +
103V GLY* 1.3 58.3 + - - +
104V PHE* 3.6 30.7 - - + -
111V GLN* 3.7 18.8 - - - +
113V VAL 3.2 8.7 - - - +
114V SER* 3.6 20.4 - - - +
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Residues in contact with GLY 103 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33V LEU* 3.7 21.3 - - - -
38V TRP* 4.3 4.5 - - - -
39V VAL 3.3 6.7 - - - -
102V ILE* 1.3 76.0 - - - +
104V PHE* 1.3 61.6 + - - -
111V GLN* 3.2 6.3 - - - -
112V CYS 3.0 27.7 + - - -
113V VAL* 3.0 15.3 + - - +
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Residues in contact with PHE 104 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ASN* 4.1 12.6 - - - -
187A ARG* 3.7 35.0 - - - -
37V LYS 4.8 0.3 - - - +
38V TRP* 3.3 8.0 - - - -
39V VAL* 2.8 53.3 + - + +
41V CYS* 3.7 27.1 - - + -
69V MET* 5.4 0.7 - - + -
73V PRO* 4.1 22.0 - - + -
75V PHE* 6.2 0.9 - + - -
102V ILE* 3.6 16.4 - - + -
103V GLY* 1.3 74.1 - - - -
105V ASP* 1.3 63.2 + - - +
106V SER* 3.8 4.9 + - - +
109V GLN 6.1 1.8 - - - -
110V VAL 4.0 4.9 - - - -
111V GLN* 3.8 24.0 - - + -
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Residues in contact with ASP 105 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37V LYS 5.9 0.2 - - - -
38V TRP* 3.5 24.1 + - + -
103V GLY 4.0 0.4 + - - -
104V PHE* 1.3 73.6 - - - +
106V SER* 1.3 52.4 + - - +
107V ASN* 3.1 25.7 + - - +
108V ARG* 3.4 27.3 + - - +
109V GLN* 2.7 36.4 + - - -
110V VAL* 3.0 19.8 + - + +
112V CYS* 3.6 18.9 - - - -
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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