Contacts of the strand formed by residues 170 - 176 (chain A) in PDB entry 1JQI
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 ALA 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A TYR* 3.5 27.6 - - + +
115A TRP* 3.8 15.0 - - + -
119A PHE* 3.6 13.9 - - + -
126A GLY* 3.4 4.7 - - - -
127A CYS* 3.2 24.3 + - - -
168A ALA* 3.5 2.8 - - - +
169A SER* 1.3 83.4 - - - +
171A THR* 1.3 62.7 + - - +
191A VAL 3.2 13.0 - - - +
193A MET* 3.7 6.8 - - - +
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Residues in contact with THR 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A TYR* 4.6 2.9 - - - -
127A CYS* 3.3 33.6 + - - -
129A ALA* 3.9 11.8 - - - +
170A ALA* 1.3 76.1 - - - +
172A VAL* 1.3 70.0 + - - +
173A VAL* 4.7 7.9 - - + -
189A PHE 3.4 2.4 - - - +
190A LEU* 3.6 3.6 - - - +
191A VAL* 2.9 55.3 + - + +
193A MET* 3.8 13.0 - - + -
198A LEU* 5.3 0.9 - - + -
217A LEU* 4.2 12.7 - - + +
219A PHE* 4.9 3.4 - - + -
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Residues in contact with VAL 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU 4.4 2.0 - - - +
99A TYR* 4.0 31.6 - - + +
102A PRO* 4.4 11.4 - - + -
103A ILE* 4.4 1.1 - - + -
127A CYS 3.2 7.3 + - - +
128A PHE* 3.9 9.3 - - + -
129A ALA 3.0 23.2 + - - +
171A THR* 1.3 74.7 + - - +
173A VAL* 1.3 60.4 + - - +
174A PHE* 3.9 27.6 - - + -
188A ALA* 4.5 5.8 - - + -
189A PHE 3.4 7.6 - - - +
190A LEU* 3.8 21.5 - - + -
230A LEU* 4.5 17.5 - - + -
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Residues in contact with VAL 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ALA* 3.6 17.3 - - + +
144A THR* 5.0 5.2 - - + -
155A LEU* 3.9 13.5 - - + -
159A LYS* 4.1 8.3 - - + -
171A THR* 3.7 3.6 + - + -
172A VAL* 1.3 73.4 - - - +
174A PHE* 1.3 75.6 + - - +
175A ALA* 5.1 0.9 - - + -
187A SER 3.7 0.5 - - - +
188A ALA* 3.4 2.3 - - - -
189A PHE* 2.8 53.1 + - + +
191A VAL* 3.6 25.4 - - + -
219A PHE* 4.1 27.4 - - + -
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Residues in contact with PHE 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A PHE* 3.3 38.1 - + - -
129A ALA 3.2 14.9 + - - +
130A LEU* 4.0 27.1 - - + -
142A ALA* 4.6 3.2 - - + +
144A THR* 4.4 0.3 - - - -
159A LYS* 2.8 31.4 + - - +
172A VAL* 3.9 24.7 - - + -
173A VAL* 1.3 77.2 - - - +
175A ALA* 1.3 60.8 + - - +
186A ILE* 4.1 10.3 - - + -
187A SER 3.5 2.0 - - - -
188A ALA* 3.7 22.4 - - + -
236A GLY* 3.3 31.6 - - - -
239A ILE* 4.2 7.4 - - + -
240A ALA* 3.6 21.1 - - + -
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Residues in contact with ALA 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ALA* 4.9 2.0 - - - -
144A THR* 3.3 28.0 - - + +
145A THR 4.0 11.9 - - - -
146A ALA* 4.0 12.1 - - + -
155A LEU* 5.1 4.7 - - + -
173A VAL* 4.0 3.9 + - + -
174A PHE* 1.3 75.0 - - - +
176A SER* 1.3 61.7 + - - +
177A THR* 3.6 0.9 + - - +
186A ILE* 3.4 6.3 - - - +
187A SER* 2.8 35.2 + - - +
189A PHE* 4.1 8.7 - - + -
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Residues in contact with SER 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ALA* 4.0 19.1 - - - +
144A THR 2.7 17.6 + - - -
145A THR* 3.4 14.9 - - - +
146A ALA 2.9 23.6 + - - +
175A ALA* 1.3 71.4 - - - +
177A THR* 1.3 61.6 + - - +
178A ASP 3.8 0.7 + - - -
179A ARG* 3.7 25.8 + - - +
182A GLN 5.4 1.4 + - - -
185A GLY 3.4 11.7 + - - -
186A ILE* 4.4 6.3 - - - +
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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