Contacts of the strand formed by residues 113 - 122 (chain B) in PDB entry 5I2Y
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 ARG 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A LEU* 5.5 0.4 - - - -
213A PRO* 3.9 30.4 - - - +
98B TRP* 3.7 62.3 + - + +
101B GLU* 5.9 2.2 - - - +
102B LEU* 4.7 15.7 - - + +
109B PRO* 3.4 25.1 - - + +
111B SER* 3.1 28.6 + - - +
112B PRO* 1.3 83.6 + - - +
114B ALA* 1.3 59.7 + - - +
182B LEU 3.5 1.6 - - - +
183B LEU* 3.4 5.7 - - - -
184B LEU* 2.7 45.7 + - + +
187B CYS* 5.1 8.3 - - - -
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Residues in contact with ALA 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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212A LEU* 4.3 17.2 - - + +
213A PRO* 5.8 0.4 - - - +
95B LEU* 3.8 36.7 - - + +
98B TRP* 2.7 30.7 + - - +
113B ARG* 1.3 73.5 - - - +
115B GLY* 1.3 54.8 + - - +
148B ASP* 5.1 0.3 - - - +
181B LEU* 5.2 2.2 - - + -
182B LEU 3.4 7.2 - - - +
183B LEU* 4.2 2.6 - - + +
212B LEU* 4.3 19.7 - - + -
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Residues in contact with GLY 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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93A LEU* 4.5 3.8 - - - -
98B TRP* 4.3 5.4 - - - -
113B ARG 4.1 0.4 + - - -
114B ALA* 1.3 75.1 - - - +
116B GLN* 1.3 60.3 + - - -
146B VAL* 4.0 13.7 - - - +
147B SER 3.1 13.2 - - - -
181B LEU* 3.3 9.5 - - - -
182B LEU* 2.7 36.3 + - - +
184B LEU* 5.5 0.4 - - - +
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Residues in contact with GLN 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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93A LEU* 3.5 33.2 - - + +
115B GLY* 1.3 73.1 - - - -
117B LEU* 1.3 68.7 - - - +
118B LEU* 3.3 15.7 + - - +
146B VAL* 3.2 7.3 - - - -
147B SER* 2.7 39.2 + - - +
179B GLY* 3.1 23.5 + - - +
180B ARG 3.5 4.3 - - - +
181B LEU* 3.8 7.1 - - + +
182B LEU* 5.1 0.2 - - - -
216B GLN* 2.8 34.5 + - - +
217B PRO 3.4 11.1 + - - +
218B ARG* 3.6 16.0 - - - +
219B LEU 4.5 1.9 + - - -
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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 GLY 4.0 1.0 + - - -
116B GLN* 1.3 72.2 - - - +
118B LEU* 1.3 59.7 + - - +
119B GLU 3.8 24.7 - - - +
120B VAL* 4.0 15.5 - - + -
144B LEU* 3.9 33.7 - - + -
145B LEU 4.0 2.9 - - - +
146B VAL* 4.8 3.6 - - + +
174B PHE* 4.1 7.9 - - + +
177B THR* 3.2 43.3 - - - +
178B GLU* 3.7 7.9 - - + +
179B GLY* 3.0 24.3 + - - -
180B ARG 2.9 17.6 + - - +
182B LEU* 4.6 14.4 - - + +
218B ARG* 3.7 3.5 - - - -
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Residues in contact with LEU 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 GLN* 3.3 25.3 + - + +
117B LEU* 1.3 74.6 - - - +
119B GLU* 1.3 70.0 + - + +
145B LEU* 2.8 27.5 + - + +
147B SER* 3.8 29.4 - - - +
152B SER* 4.5 10.5 - - - -
178B GLU* 4.1 1.9 - - - +
218B ARG* 2.9 52.1 + - + +
219B LEU 4.1 18.6 - - - +
220B ARG* 5.6 0.9 - - - -
221B VAL* 4.2 13.7 - - + +
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Residues in contact with GLU 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 4.1 - - - +
118B LEU* 1.3 91.8 - - + +
120B VAL* 1.3 63.6 + - - +
121B LEU* 3.6 19.7 + - + +
144B LEU* 3.6 3.5 - - - -
145B LEU* 2.8 49.9 + - + +
178B GLU* 4.6 4.9 - - - -
218B ARG* 4.7 6.1 - - - +
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Residues in contact with VAL 120 (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* 4.0 13.0 - - + -
119B GLU* 1.3 74.5 - - - +
121B LEU* 1.3 60.8 + - - +
122B GLN 3.9 5.4 - - - +
123B ASP* 3.9 37.2 - - - +
143B THR 4.0 2.2 - - - -
144B LEU* 3.9 12.3 - - + -
174B PHE* 3.8 28.3 - - + +
175B ARG* 2.8 40.7 + - + +
178B GLU* 3.7 21.1 + - - +
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Residues in contact with LEU 121 (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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119B GLU* 4.2 30.7 - - + +
120B VAL* 1.3 73.4 - - - +
122B GLN* 1.3 63.5 + - - +
143B THR* 3.0 27.9 + - + +
145B LEU* 4.4 16.4 - - + +
154B ARG* 4.0 31.6 - - + -
175B ARG* 3.4 11.5 + - - -
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Residues in contact with GLN 122 (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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120B VAL* 3.9 5.2 - - - +
121B LEU* 1.3 80.8 + - - +
123B ASP* 1.3 78.2 + - - +
140B VAL* 5.7 7.0 - - + -
141B GLY 4.3 9.2 - - - +
142B ALA* 3.3 3.6 - - - +
143B THR* 2.9 46.9 + - - +
175B ARG* 4.6 1.5 - - - +
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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