Contacts of the strand formed by residues 169 - 179 (chain B) in PDB entry 1GQC
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 TYR 169 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128B ALA* 3.5 4.7 - - - +
129B ILE* 3.3 44.4 + - + +
131B ALA* 3.7 36.8 - - + +
134B ALA* 3.5 21.8 - - + -
141B LYS* 4.6 2.7 - - + -
157B PRO* 4.2 7.1 + - + +
158B ILE 3.6 27.6 - - - -
159B PRO* 2.9 30.2 + - + -
161B PRO* 3.7 19.9 - - - +
167B ALA* 3.7 27.2 - - + +
168B ARG* 1.3 78.8 - - - +
170B LEU* 1.3 71.1 + - - +
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Residues in contact with LEU 170 (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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193A MET* 6.5 2.0 - - + -
126B CYS* 4.1 19.7 - - + -
127B HIS 3.6 4.7 - - - +
128B ALA* 3.8 21.3 - - + +
129B ILE* 4.3 4.7 - - - +
141B LYS* 3.3 11.0 - - - +
142B VAL* 3.1 48.7 + - + +
143B VAL* 5.5 0.2 - - - -
144B VAL* 4.2 29.2 - - + +
158B ILE 5.5 0.8 + - - -
168B ARG 5.2 3.4 - - - +
169B TYR* 1.3 85.8 - - - +
171B LYS* 1.3 59.2 + - - +
216B GLU* 4.3 20.0 - - - +
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Residues in contact with LYS 171 (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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126B CYS* 3.1 7.9 - - - +
127B HIS* 2.8 55.5 + - + +
129B ILE* 3.4 29.4 - - + +
139B THR* 3.7 30.7 + - + +
140B VAL 3.3 8.5 - - - +
142B VAL* 4.7 0.2 - - - -
170B LEU* 1.3 72.4 - - - +
172B HIS* 1.3 75.1 + - - +
173B VAL* 3.7 2.6 + - + +
220B THR* 5.6 2.7 - - - -
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Residues in contact with HIS 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B THR* 2.8 41.8 - - + +
125B LEU 3.1 14.3 + - - -
126B CYS* 4.4 3.3 - - - +
140B VAL* 3.0 29.3 + - + +
142B VAL* 4.5 7.8 - - + +
153B PHE* 3.4 27.1 - + + -
170B LEU 3.9 0.2 + - - -
171B LYS* 1.3 86.1 - - - +
173B VAL* 1.3 70.3 + - - +
174B GLY* 3.7 5.0 + - - -
176B TYR* 3.3 25.8 + + - -
202B GLN* 3.2 24.7 - - - -
214B THR* 5.9 0.2 - - - +
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Residues in contact with VAL 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B GLU* 4.7 8.7 - - - +
124B THR* 3.2 15.9 + - - -
125B LEU* 2.9 25.8 + - + +
126B CYS* 4.2 12.3 - - - +
127B HIS* 3.6 31.9 - - + -
171B LYS* 4.2 4.0 - - + +
172B HIS* 1.3 75.1 - - - +
174B GLY* 1.3 52.9 + - - +
175B ILE* 2.7 41.4 + - + -
217B VAL* 5.0 0.7 - - + -
220B THR* 3.9 25.8 - - + +
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Residues in contact with GLY 174 (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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96B GLN* 3.1 38.1 + - - +
99B GLU* 4.9 6.7 + - - -
172B HIS* 3.7 10.6 + - - -
173B VAL* 1.3 70.5 - - - +
175B ILE* 1.3 61.3 + - - -
176B TYR* 3.7 18.6 - - - -
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Residues in contact with ILE 175 (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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93B ILE* 4.5 4.0 - - + -
94B ASN 3.7 11.9 - - - +
95B LEU* 3.8 21.1 - - + -
96B GLN* 5.5 1.8 - - + +
99B GLU* 4.7 7.9 - - - +
102B ILE* 3.2 35.4 - - + -
107B VAL* 4.9 3.8 - - + -
110B LEU* 3.7 23.6 - - + -
124B THR* 2.6 29.6 + - - -
125B LEU* 3.4 29.2 - - + -
173B VAL* 2.7 22.9 + - + -
174B GLY* 1.3 77.5 - - - +
176B TYR* 1.3 62.7 + - - +
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Residues in contact with TYR 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B THR* 6.1 1.3 - - - -
93B ILE* 3.1 6.2 - - - +
94B ASN* 2.6 51.2 + - + -
96B GLN* 5.1 3.4 - - - -
110B LEU* 4.1 3.4 - - - -
122B VAL* 4.2 18.4 - - + -
123B ALA 3.5 3.4 - - - +
124B THR* 4.3 9.2 - - + -
153B PHE* 5.9 0.4 - + - -
172B HIS* 3.3 25.1 + - - -
174B GLY* 3.7 23.6 - - - -
175B ILE* 1.3 79.6 - - - +
177B ALA* 1.3 61.8 + - - +
178B TYR* 3.6 36.8 - + + -
202B GLN* 3.5 37.0 + - + +
205B LEU* 5.3 2.5 - - + -
212B ILE* 5.1 5.4 - - + -
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Residues in contact with ALA 177 (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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91B ILE* 4.6 1.8 - - + -
92B TYR 3.3 5.8 - - - +
93B ILE* 4.2 11.2 - - + +
110B LEU* 3.8 24.7 - - + -
111B LEU* 5.5 0.4 - - - +
114B MET* 3.7 30.0 - - + +
122B VAL* 3.3 8.0 - - - +
123B ALA* 3.0 32.1 + - + +
176B TYR* 1.3 73.6 - - - +
178B TYR* 1.3 59.5 + - - +
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Residues in contact with TYR 178 (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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77B THR* 4.1 19.1 + - + +
80B LEU* 3.6 32.1 - - + -
91B ILE* 3.4 4.4 - - - +
92B TYR* 2.7 42.1 + - - +
94B ASN* 4.3 6.4 + - + -
114B MET* 3.7 4.9 - - - +
121B PRO 3.7 1.6 - - - -
122B VAL* 3.7 32.8 - - + -
176B TYR* 3.6 39.9 - - + -
177B ALA* 1.3 75.9 - - - +
179B ARG* 1.3 70.6 + - - +
182B VAL* 4.1 13.0 - - + -
183B LEU* 4.0 20.9 - - + -
186B TYR* 5.7 3.9 - + - -
205B LEU* 4.2 16.0 - - + +
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Residues in contact with ARG 179 (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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1B SER* 4.2 8.7 + - - -
90B ASP* 3.7 7.1 + - - +
91B ILE* 4.1 23.6 - - - +
114B MET* 3.0 46.0 + - - +
115B ARG* 4.7 2.0 - - - +
117B ASP 3.2 10.1 + - - -
118B PRO* 3.4 30.9 + - - +
120B LEU 3.2 26.1 + - - -
121B PRO* 3.0 20.4 + - + +
178B TYR* 1.3 79.5 - - - +
180B ARG* 1.3 68.4 + - - +
181B ASP* 3.4 23.8 - - - +
182B VAL* 3.2 15.2 + - + +
183B LEU* 3.6 4.5 + - - +
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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