Contacts of the strand formed by residues 112 - 119 (chain B) in PDB entry 1TYE
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 112 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B TYR 3.3 16.8 - - - +
111B PRO* 1.3 75.0 - - - +
113B ASP* 1.3 74.2 + - - +
114B ILE* 4.3 3.6 - - + -
142B MET* 3.6 25.6 - - + -
146B THR* 3.6 16.8 - - + -
148B ASN 3.3 6.9 + - - -
149B LEU* 3.1 22.2 - - + +
150B ARG 3.3 8.0 + - - -
239B ARG* 3.6 1.1 + - - +
243B SER* 3.6 9.6 - - - +
245B LEU* 4.3 20.4 - - + -
348B TYR* 3.7 20.9 - - + -
351B ILE* 4.4 8.1 - - + -
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Residues in contact with ASP 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B VAL* 1.3 73.3 - - - +
114B ILE* 1.3 58.5 + - - +
150B ARG* 3.4 11.2 - - - +
196B LEU* 3.4 16.4 - - + +
237B GLY 3.8 0.3 - - - +
238B TRP* 3.7 19.1 - - + -
239B ARG* 2.6 68.7 + - - +
242B ALA* 3.9 1.6 - - - +
243B SER 2.8 14.7 + - - +
244B HIS* 3.6 6.2 - - + -
245B LEU* 2.7 35.9 + - - +
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Residues in contact with ILE 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B VAL* 4.3 1.3 + - + -
113B ASP* 1.3 78.8 - - - +
115B TYR* 1.3 66.1 + - - +
116B TYR* 4.1 0.7 - - + +
138B LEU* 4.3 24.7 - - + +
142B MET* 3.3 36.3 - - + -
149B LEU* 4.3 6.7 - - + +
150B ARG 3.3 6.5 + - - -
151B ILE* 3.3 20.2 - - + +
152B GLY 3.1 23.6 + - - -
196B LEU* 3.2 6.4 - - - +
238B TRP* 4.7 0.2 - - - -
245B LEU* 3.2 19.7 - - + +
247B VAL* 4.2 22.0 - - + -
344B ILE* 4.1 18.4 - - + -
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Residues in contact with TYR 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ILE* 1.3 75.2 - - - +
116B TYR* 1.3 61.2 + - - +
117B LEU* 3.4 26.0 - - + -
152B GLY* 3.5 6.3 - - - -
153B PHE 3.5 28.9 - - - -
154B GLY* 3.3 14.0 - - - -
190B TYR* 2.8 13.3 + - - -
192B HIS* 2.7 39.3 + + - -
194B LEU 3.9 1.3 - - - -
196B LEU* 4.3 4.5 - - + -
229B ALA* 3.7 25.1 - - + -
236B ILE* 3.7 22.2 - - + -
238B TRP* 3.6 24.2 - - + -
245B LEU 3.0 7.7 + - - -
246B LEU* 3.5 10.2 - - + +
247B VAL 3.1 25.3 + - - +
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Residues in contact with TYR 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ILE* 4.1 3.0 - - + +
115B TYR* 1.3 75.1 - - - +
117B LEU* 1.3 66.8 + - - +
118B MET* 3.6 33.0 - - + -
131B ILE* 2.7 42.0 + - + +
134B LEU* 3.1 26.7 - - + +
135B GLY* 3.5 19.1 - - - -
138B LEU* 3.8 22.2 - - + -
151B ILE* 5.8 0.4 - - + -
152B GLY 2.9 9.6 + - - +
153B PHE* 3.1 16.8 - - + +
154B GLY 2.8 27.5 + - - +
203B PHE* 4.5 9.2 - + + -
207B VAL* 5.0 2.2 - - + -
247B VAL* 3.6 13.0 - - + -
249B THR* 3.6 23.0 - - + +
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Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B TYR* 3.4 32.1 - - + -
116B TYR* 1.3 74.3 - - - +
118B MET* 1.3 57.0 + - - +
119B ASP 3.8 0.3 + - - -
154B GLY 4.1 4.7 - - - +
156B PHE* 4.1 8.5 - - + -
190B TYR* 3.9 21.5 - - + -
225B ALA* 3.7 25.8 - - + +
226B ILE* 3.7 32.3 - - + +
229B ALA* 4.3 2.9 - - + -
246B LEU* 4.2 11.9 - - + -
247B VAL 2.9 17.2 + - - +
248B PHE* 3.8 11.6 - - + -
249B THR* 2.8 34.3 + - - +
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Residues in contact with MET 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B TYR* 3.6 30.1 - - + -
117B LEU* 1.3 71.4 - - - +
119B ASP* 1.3 61.8 + - - +
120B LEU* 3.2 20.1 + - + -
128B LEU* 4.7 0.7 - - + -
131B ILE* 3.6 30.1 - - + -
132B GLN* 4.4 5.2 - - + -
153B PHE* 3.4 33.0 - - + -
154B GLY 2.8 16.4 + - - +
155B ALA* 3.2 6.2 - - + +
156B PHE* 2.9 30.1 + - - -
207B VAL* 4.1 21.8 - - + +
210B GLN* 4.1 16.2 - - + -
249B THR* 3.6 3.4 - - - -
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Residues in contact with ASP 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B LEU 3.8 0.8 + - - -
118B MET* 1.3 69.4 - - - +
120B LEU* 1.3 65.7 + - - +
121B SER* 2.7 31.0 + - - -
124B MET* 3.0 41.5 - - + +
131B ILE* 3.7 1.1 - - - +
156B PHE* 3.5 25.5 - - + +
220B GLU* 4.1 7.4 - - - +
249B THR* 3.2 26.2 + - - +
250B THR* 3.0 25.2 + - - -
251B ASP* 3.9 4.0 - - - +
252B ALA* 5.4 0.2 - - - +
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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