Contacts of the strand formed by residues 110 - 118 (chain T) 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 VAL 110 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155B ILE* 5.7 1.3 - - + -
156B GLN* 3.4 42.8 - - + +
159B ARG* 5.5 9.6 - - + -
160B ASP* 5.5 3.4 - - - +
165B TYR* 5.7 1.8 - - + -
104T PHE* 4.8 3.3 - - - -
105T ASP* 3.0 23.7 + - + +
108T ARG* 3.5 58.1 - - + +
109T GLN* 1.3 76.0 - - - +
111T GLN* 1.3 66.5 + - - +
112T CYS* 3.3 9.8 + - - -
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Residues in contact with GLN 111 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B ARG* 5.1 3.3 - - - -
160B ASP* 5.4 2.2 + - - +
165B TYR* 3.2 64.5 - - + +
166B GLY 4.6 0.5 + - - -
183C LYS* 4.0 9.5 - - - +
187C ARG* 2.9 34.0 + - - +
43T GLU* 5.3 1.4 + - - -
100T ARG* 6.0 0.4 - - - +
102T ILE* 3.8 31.6 - - + +
103T GLY 3.3 11.7 - - - +
104T PHE* 3.8 19.5 - - + +
110T VAL* 1.3 73.9 - - - +
112T CYS* 1.3 59.3 + - - +
113T VAL 3.4 6.1 - - - +
114T SER* 4.4 1.4 + - - -
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Residues in contact with CYS 112 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B GLY* 3.4 22.4 - - - +
396B ASP* 4.5 7.9 - - - +
32T TYR* 5.4 1.0 + - - -
38T TRP* 3.7 40.6 - - + -
103T GLY 2.9 7.2 + - - +
105T ASP* 3.6 31.6 - - - -
108T ARG* 3.7 25.4 - - - -
110T VAL* 3.3 4.7 + - - -
111T GLN* 1.3 72.6 - - - +
113T VAL* 1.3 66.3 + - - +
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Residues in contact with VAL 113 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B TYR* 4.7 2.0 - - - -
166B GLY* 4.5 4.9 - - - -
432B ASN* 5.7 1.1 - - - +
29T GLN* 5.5 2.7 - - - +
32T TYR* 4.0 19.1 - - + -
33T LEU* 4.2 20.0 - - + -
38T TRP* 3.7 26.2 - - + -
101T ILE 4.4 2.7 - - - +
102T ILE* 3.2 4.3 - - - +
103T GLY* 3.0 32.1 + - - +
111T GLN* 3.4 4.6 - - - +
112T CYS* 1.3 86.5 - - - +
114T SER* 1.3 69.0 + - - +
115T PHE* 3.7 30.5 - - + -
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Residues in contact with SER 114 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B TYR* 4.0 35.8 + - - +
166B GLY* 5.0 0.8 - - - -
13T GLU* 5.5 2.6 - - - +
14T THR* 3.8 22.9 + - - +
100T ARG* 3.7 22.2 - - - -
101T ILE 3.3 7.6 - - - -
102T ILE* 3.8 8.5 - - - +
111T GLN* 4.4 1.0 + - - -
113T VAL* 1.3 80.3 - - - +
115T PHE* 1.3 66.9 + - - +
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Residues in contact with PHE 115 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12T TYR 5.2 2.2 - - - -
14T THR* 3.7 19.3 - - + +
15T LEU* 4.2 17.0 - - + -
21T LEU* 4.5 13.0 - - + -
26T LEU* 3.6 27.6 - - + -
29T GLN* 3.9 30.5 - - + -
30T VAL* 4.8 5.2 - - + -
33T LEU* 5.5 1.1 - - + -
100T ARG* 4.4 2.4 - - - +
101T ILE* 3.1 56.0 + - + -
113T VAL* 3.7 28.9 - - + -
114T SER* 1.3 76.1 + - - +
116T ILE* 1.3 79.4 + - - +
117T ALA* 3.4 1.3 + - + -
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Residues in contact with ILE 116 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12T TYR* 3.7 46.6 + - + +
14T THR 5.1 0.6 + - - -
21T LEU* 5.2 4.9 - - - +
67T TRP* 4.4 18.4 - - + -
98T PHE* 5.1 2.2 - - + -
99T ILE 3.6 8.1 - - - +
100T ARG* 4.3 20.6 - - - +
115T PHE* 1.3 83.0 - - - +
117T ALA* 1.3 61.7 + - - +
118T TYR* 3.5 24.0 - - - +
119T LYS* 3.5 24.0 - - + -
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Residues in contact with ALA 117 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26T LEU* 4.3 14.8 - - + +
87T LEU* 4.0 24.6 - - + +
91T LYS* 5.8 0.5 - - - +
99T ILE 2.8 9.1 + - - +
101T ILE* 3.7 35.9 - - + -
115T PHE* 3.4 4.8 + - + -
116T ILE* 1.3 75.5 - - - +
118T TYR* 1.3 63.6 + - - +
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Residues in contact with TYR 118 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87T LEU* 4.7 1.8 - - + -
91T LYS* 3.6 39.3 - - + -
94T TYR 4.1 4.0 - - - -
95T PRO* 2.7 38.8 + - + +
97T ALA 3.2 28.7 - - - -
98T PHE* 3.5 3.3 - - - -
99T ILE* 2.9 52.5 + - + -
116T ILE* 3.5 8.3 - - - +
117T ALA* 1.3 82.1 - - - +
119T LYS* 1.3 82.0 + - - +
120T PRO* 4.3 2.3 - - - +
121T ALA 5.3 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