Contacts of the strand formed by residues 110 - 118 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A ILE* 6.0 1.1 - - + -
156A GLN* 3.7 27.8 - - + +
159A ARG* 5.5 10.1 - - + -
160A ASP* 5.5 4.7 - - - +
165A TYR* 5.7 1.6 - - + -
104S PHE* 4.8 2.9 - - - -
105S ASP* 3.0 23.9 + - + +
108S ARG* 3.2 65.1 - - + +
109S GLN* 1.3 77.7 - - - +
111S GLN* 1.3 66.7 + - - +
112S CYS* 3.4 12.2 + - - -
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Residues in contact with GLN 111 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ARG* 5.0 3.3 - - - -
160A ASP* 5.4 1.3 + - - +
165A TYR* 3.1 64.9 - - + +
166A GLY 4.6 0.2 + - - -
183B LYS* 3.8 9.4 + - - +
187B ARG* 3.0 33.9 + - - +
43S GLU* 5.3 1.4 + - - -
102S ILE* 3.7 32.1 - - + +
103S GLY 3.3 11.2 - - - +
104S PHE* 3.7 21.1 - - + +
110S VAL* 1.3 75.6 - - - +
112S CYS* 1.3 60.9 + - - +
113S VAL 3.4 4.9 - - - +
114S SER* 4.3 2.4 + - - -
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Residues in contact with CYS 112 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A GLY* 3.3 23.3 - - - +
396A ASP* 4.5 7.2 - - - +
32S TYR* 5.4 1.4 - - - -
38S TRP* 3.6 41.7 - - + -
103S GLY 3.0 6.6 + - - +
105S ASP* 3.6 31.4 - - - -
108S ARG* 3.7 14.1 - - - -
110S VAL* 3.6 15.7 - - - -
111S GLN* 1.3 72.4 - - - +
113S VAL* 1.3 65.9 + - - +
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Residues in contact with VAL 113 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A TYR* 4.7 1.6 - - - -
166A GLY* 4.6 3.8 - - - -
432A ASN* 5.8 0.9 - - - +
29S GLN* 5.4 4.0 - - - +
32S TYR* 4.2 15.9 - - + -
33S LEU* 4.0 22.4 - - + -
38S TRP* 3.5 28.9 - - + -
101S ILE 4.4 2.0 - - - +
102S ILE* 3.1 4.5 - - - +
103S GLY* 2.9 31.0 + - - +
111S GLN* 3.4 4.3 - - - +
112S CYS* 1.3 86.7 - - - +
114S SER* 1.3 69.4 + - - +
115S PHE* 3.7 29.8 - - + -
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Residues in contact with SER 114 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A TYR* 4.0 35.2 + - - +
166A GLY* 5.0 0.8 - - - -
13S GLU* 5.4 2.9 - - - +
14S THR* 3.7 23.4 + - - +
100S ARG* 4.2 12.8 + - - -
101S ILE 3.3 7.6 - - - -
102S ILE* 3.7 16.7 - - - +
111S GLN* 4.3 1.1 + - - -
113S VAL* 1.3 81.5 - - - +
115S PHE* 1.3 64.6 + - - +
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Residues in contact with PHE 115 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12S TYR 5.3 2.9 - - - -
14S THR* 3.6 20.0 - - + +
15S LEU* 4.2 15.9 - - + -
21S LEU* 4.3 19.1 - - + -
26S LEU* 3.8 26.5 - - + -
29S GLN* 3.8 29.4 - - + -
30S VAL* 4.8 3.8 - - + -
33S LEU* 5.5 0.9 - - + -
100S ARG* 3.3 5.1 - - - +
101S ILE* 3.0 56.4 + - + -
113S VAL* 3.7 27.1 - - + -
114S SER* 1.3 75.7 + - - +
116S ILE* 1.3 72.8 + - - +
117S ALA* 4.5 4.3 - - + -
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Residues in contact with ILE 116 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12S TYR* 4.0 35.9 + - + +
14S THR 5.0 1.0 + - - -
16S SER* 5.7 3.4 - - - -
21S LEU* 5.0 5.2 - - - +
67S TRP* 3.6 31.6 - - + -
98S PHE* 4.0 7.2 - - + -
99S ILE 3.3 25.8 - - - +
100S ARG* 3.9 4.0 - - + +
115S PHE* 1.3 80.6 - - - +
117S ALA* 1.3 58.6 + - - +
118S TYR 3.6 13.0 - - - +
119S LYS* 3.3 37.5 - - + +
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Residues in contact with ALA 117 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21S LEU* 6.2 0.9 - - - -
26S LEU* 4.8 11.4 - - + +
87S LEU* 4.1 24.3 - - + +
91S LYS* 5.6 1.0 + - - +
99S ILE 2.8 9.8 + - - +
101S ILE* 3.9 33.7 - - + -
115S PHE* 3.5 9.5 + - + -
116S ILE* 1.3 73.5 - - - +
118S TYR* 1.3 63.1 + - - +
119S LYS* 6.2 0.2 - - - -
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Residues in contact with TYR 118 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87S LEU* 4.7 1.3 - - + -
91S LYS* 3.6 40.8 - - + -
94S TYR 4.1 4.5 - - - -
95S PRO* 2.7 39.2 + - + +
97S ALA 3.2 27.8 - - - -
98S PHE* 3.5 2.9 - - - -
99S ILE* 2.9 53.3 + - + +
116S ILE* 3.6 6.8 - - - +
117S ALA* 1.3 82.5 - - - +
119S LYS* 1.3 82.7 + - - +
120S PRO* 4.4 1.9 - - - +
121S ALA 5.3 0.7 + - - -
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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