Contacts of the strand formed by residues 178 - 188 (chain B) in PDB entry 3QI5
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 CYS 178 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ALA* 4.1 1.7 - - - +
126B ALA* 3.9 0.2 - - - -
127B TYR* 2.9 37.0 + - - +
149B MET* 3.6 35.9 - - + -
157B TYR* 5.6 0.9 - - + -
169B ASN* 3.5 32.5 - - + -
170B ILE 3.3 19.5 - - - +
171B SER* 4.0 3.1 - - - +
172B SER* 3.7 3.8 + - - +
177B ALA* 1.3 75.8 - - - +
179B VAL* 1.3 67.6 + - - +
7E EDC 3.9 9.2 - - - -
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Residues in contact with VAL 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ALA* 3.5 28.9 - - + +
98B LEU* 4.1 16.6 - - + -
99B ALA* 3.7 19.7 - - + +
102B PHE* 3.7 27.6 - - + -
124B THR* 3.9 6.3 - - + -
125B GLU 3.3 11.9 - - - +
126B ALA* 4.7 0.2 - - - -
169B ASN* 3.1 5.8 - - - -
170B ILE* 2.8 42.2 + - - +
172B SER* 4.7 0.4 - - - -
178B CYS* 1.3 80.0 - - - +
180B LEU* 1.3 72.5 + - - +
181B LEU* 3.8 1.6 + - + -
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Residues in contact with LEU 180 (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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124B THR* 3.3 9.7 - - - -
125B GLU* 3.0 53.8 + - + +
127B TYR* 4.1 9.1 - - + -
167B CYS* 3.9 21.8 - - + -
168B MET 3.5 17.7 - - - +
169B ASN* 3.3 17.6 - - - +
178B CYS 4.3 0.4 + - - -
179B VAL* 1.3 73.2 - - - +
181B LEU* 1.3 71.1 + - - +
182B ARG* 3.7 18.8 + - + +
218B PRO* 4.1 9.9 - - + -
7E EDC 3.3 35.7 - - + +
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Residues in contact with LEU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B PHE* 4.2 13.9 - - + -
107B LEU* 3.8 30.1 - - + -
121B ILE* 3.8 32.1 - - + -
123B GLU 4.1 1.8 - - - +
124B THR* 3.9 19.3 - - + -
168B MET* 3.2 22.5 + - + +
170B ILE* 3.7 29.6 - - + -
179B VAL* 3.8 0.4 + - + -
180B LEU* 1.3 81.9 - - - +
182B ARG* 1.3 59.5 + - - +
183B ALA 3.8 0.7 - - - +
184B LEU* 5.0 4.0 - - + -
218B PRO* 3.6 17.3 - - - +
221B LEU* 3.6 17.1 - - + +
236B LEU* 6.0 0.7 - - + -
244B LEU* 5.9 0.2 - - + -
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Residues in contact with ARG 182 (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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123B GLU* 2.9 47.5 + - + +
124B THR 4.8 0.4 - - - -
125B GLU* 3.4 34.3 + - + -
180B LEU* 3.7 23.2 + - + +
181B LEU* 1.3 72.6 - - - +
183B ALA* 1.3 61.6 + - - +
217B GLY* 2.9 31.7 + - - -
218B PRO* 3.1 19.2 - - + +
221B LEU* 3.6 4.9 - - - -
262B VAL* 3.7 34.7 + - - +
276B ARG* 4.1 0.9 - - - +
286B SER* 3.0 23.2 + - - -
287B VAL* 4.2 4.8 - - - +
7E EDC 3.8 5.7 + - - -
8E T 2.8 27.1 + - - -
9E T 4.7 3.2 + - - -
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Residues in contact with ALA 183 (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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121B ILE* 3.7 1.6 - - - +
122B VAL* 3.1 25.1 + - + -
123B GLU* 3.4 30.9 + - + +
182B ARG* 1.3 80.6 + - - +
184B LEU* 1.3 72.8 + - - +
215B CYS 3.2 10.3 - - - +
217B GLY 4.4 1.3 - - - +
221B LEU* 3.6 3.0 - - - +
284B TRP 3.4 22.9 - - - +
286B SER 4.0 4.3 - - - +
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Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU* 4.3 13.2 - - + -
119B GLY* 4.2 20.6 - - - +
120B ARG 3.1 7.6 - - - +
121B ILE* 3.5 31.0 - - + +
122B VAL* 4.2 5.4 - - - -
181B LEU* 5.0 3.6 - - + -
183B ALA* 1.3 84.8 - - - +
185B GLU* 1.3 59.3 + - - +
186B PRO* 3.3 11.1 - - - +
215B CYS* 3.2 26.2 + - + +
221B LEU* 4.0 25.8 - - + -
225B LEU* 3.9 39.5 - - + -
284B TRP* 3.8 9.1 - - - +
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Residues in contact with GLU 185 (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 GLY* 3.2 1.8 - - - -
120B ARG* 2.7 68.7 + - + +
122B VAL* 4.3 6.7 - - + +
184B LEU* 1.3 71.2 - - - +
186B PRO* 1.3 73.9 - - - +
187B LEU* 3.4 22.2 + - - +
249B LEU* 6.1 0.2 - - - +
284B TRP* 3.4 43.5 + - + +
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Residues in contact with PRO 186 (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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118B ARG 3.9 5.6 - - - +
119B GLY* 4.4 2.0 - - - -
184B LEU 3.3 10.5 - - - +
185B GLU* 1.3 87.8 - - + +
187B LEU* 1.3 63.2 + - - +
190B LEU* 3.8 31.5 - - + +
193B MET* 3.9 18.8 - - + -
211B ASP 4.1 11.0 - - - +
214B LEU* 4.2 9.4 - - + -
215B CYS* 4.7 8.7 - - + +
284B TRP* 3.7 32.7 - - + -
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Residues in contact with LEU 187 (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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106B VAL* 4.2 24.0 - - + -
118B ARG* 2.8 17.9 + - + +
119B GLY 4.5 0.2 - - - -
120B ARG* 3.9 26.2 - - + +
185B GLU* 3.6 42.0 - - - +
186B PRO* 1.3 74.6 - - - +
188B GLU* 1.3 63.3 + - + +
190B LEU* 3.7 7.8 - - - +
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Residues in contact with GLU 188 (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 GLU* 4.0 19.7 + - - +
117B LEU* 3.4 4.3 - - - -
118B ARG* 2.7 73.0 + - + +
187B LEU* 1.3 81.5 - - + +
189B GLY* 1.3 66.8 + - - +
190B LEU* 3.5 5.5 - - - +
193B MET* 3.5 7.3 - - - +
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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