Contacts of the strand formed by residues 164 - 172 (chain B) in PDB entry 2JG8
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 164 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B MET* 3.9 18.3 - - + +
159B ARG 3.5 15.7 - - - +
160B GLY* 4.0 2.7 - - - +
161B ARG 5.3 0.9 - - - +
162B GLU 4.2 0.6 + - - -
163B ARG* 1.3 73.5 - - - +
165B GLN* 1.3 66.8 + - - +
194B ASN* 4.3 3.4 - - - +
196B PHE* 3.7 35.4 - - + -
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Residues in contact with GLN 165 (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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158B MET* 4.2 4.0 - - - -
159B ARG* 2.8 36.5 + - - +
163B ARG* 4.6 6.3 - - + +
164B ALA* 1.3 80.9 - - - +
166B LYS* 1.3 65.7 + - - +
167B VAL* 3.6 1.9 + - - +
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Residues in contact with LYS 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ARG* 4.3 8.9 - - - +
208A SER 5.4 5.8 + - - -
211A ASP* 4.3 4.9 + - - -
156B ASN* 4.0 16.2 - - + +
157B LEU 3.5 6.7 - - - +
158B MET* 3.5 23.2 - - + +
165B GLN* 1.3 76.8 - - - +
167B VAL* 1.3 62.9 + - - +
168B VAL* 3.9 6.9 - - - +
169B THR* 2.7 41.0 + - - +
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Residues in contact with VAL 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ILE* 4.7 3.5 - - - +
100A ARG* 4.0 12.0 + - - -
115A ILE* 3.9 36.1 - - + +
157B LEU* 2.7 33.6 + - + +
158B MET 4.3 0.7 - - - -
159B ARG* 3.6 44.6 - - + +
165B GLN 4.2 0.7 - - - +
166B LYS* 1.3 77.5 - - - +
168B VAL* 1.3 70.6 + - + +
185B MET* 4.7 4.5 - - + -
187B LEU* 4.1 11.7 - - + -
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Residues in contact with VAL 168 (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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98A ILE* 3.9 22.9 - - + -
115A ILE* 4.9 0.4 - - + -
211A ASP* 3.3 23.1 - - + +
213A VAL* 4.8 0.4 - - + -
155B VAL 3.9 0.3 - - - +
156B ASN* 3.5 4.2 - - - +
157B LEU* 2.9 39.2 + - + +
166B LYS* 3.6 7.2 - - - +
167B VAL* 1.3 90.8 + - + +
169B THR* 1.3 62.9 + - - +
170B PHE* 3.6 29.4 - - + -
185B MET* 3.6 30.7 - - + -
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Residues in contact with THR 169 (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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209A GLU 3.4 25.4 - - - +
210A ALA* 3.4 2.4 - - - -
211A ASP* 2.7 40.9 + - - +
154B CYS* 4.4 6.7 - - + -
155B VAL 3.3 7.0 - - - +
156B ASN* 2.6 25.6 + - - +
166B LYS* 2.7 27.2 + - - +
168B VAL* 1.3 72.9 - - - +
170B PHE* 1.3 63.3 + - - +
171B CYS* 4.0 15.9 - - - -
200B THR* 5.2 2.0 - - + -
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Residues in contact with PHE 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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142A GLN* 4.6 9.6 - - + -
178A VAL* 5.5 9.0 - - + -
210A ALA* 4.6 0.4 - - - -
211A ASP 4.0 15.9 - - - +
213A VAL* 3.4 34.8 - - + -
145B TYR* 3.3 35.7 + + - +
153B LEU* 3.9 1.0 - - - +
154B CYS* 3.2 1.9 - - - -
155B VAL* 2.9 39.1 + - + +
157B LEU* 4.8 9.6 - - + -
168B VAL* 3.6 24.9 - - + -
169B THR* 1.3 72.6 - - - +
171B CYS* 1.3 62.8 + - - +
172B ASP 4.3 0.2 - - - -
181B THR* 5.9 1.1 - - - +
182B THR 4.4 6.3 - - - +
183B GLY* 3.8 22.4 - - - -
184B GLY 3.7 18.4 - - - -
197B LEU* 6.2 0.2 - - + -
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Residues in contact with CYS 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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144A LEU* 3.5 14.1 - - - +
176A PHE* 3.7 28.3 - - + -
178A VAL* 3.4 19.6 - - - +
209A GLU* 4.0 12.3 - - - -
210A ALA* 3.8 25.9 - - + +
211A ASP 5.6 0.2 + - - -
153B LEU 3.3 3.4 - - - -
154B CYS* 2.1 46.9 - - - -
169B THR* 4.0 3.1 - - - -
170B PHE* 1.3 74.4 - - - +
172B ASP* 1.3 60.7 + - - +
173B TYR* 4.1 0.7 - - + -
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Residues in contact with ASP 172 (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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176A PHE 3.4 7.7 - - - +
177A GLN* 3.4 4.7 - - - +
178A VAL* 3.3 26.0 + - + +
153B LEU* 2.8 24.4 + - + +
171B CYS* 1.3 73.6 - - - +
173B TYR* 1.3 62.8 + - - +
179B GLN* 2.8 30.6 + - - +
180B VAL 4.5 2.1 - - - +
181B THR* 2.7 45.8 + - + +
1224B CA 2.3 26.6 - - - -
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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