Contacts of the strand formed by residues 159 - 166 (chain C) 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 VAL 159 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155C TYR* 3.3 2.8 - - - -
156C ARG* 2.8 38.6 + - + +
157C SER 4.3 5.6 - - - +
158C GLY* 1.3 80.6 - - - +
160C LYS* 1.3 77.2 + - - +
161C VAL* 3.4 7.4 + - + +
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Residues in contact with LYS 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B GLU* 3.7 28.7 + - - +
210B GLY* 5.3 4.8 - - - +
153C LEU* 3.5 28.9 - - + +
154C LEU 3.6 10.1 - - - +
155C TYR* 3.4 26.1 - - + +
159C VAL* 1.3 80.8 - - - +
161C VAL* 1.3 65.7 + - - +
162C VAL 4.3 4.9 - - - +
163C THR* 3.3 26.2 + - - +
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Residues in contact with VAL 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B THR* 5.6 0.7 - - - +
119B ILE* 3.8 30.2 - - + +
212B ASN* 4.1 2.8 - - - +
154C LEU* 2.8 21.9 + - + +
156C ARG* 3.8 33.7 - - + +
159C VAL* 3.8 11.0 - - + +
160C LYS* 1.3 75.6 - - - +
162C VAL* 1.3 70.5 + - + +
179C VAL* 4.2 14.4 - - + -
181C LEU* 4.2 14.4 - - + -
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Residues in contact with VAL 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B THR* 4.4 7.6 - - + -
119B ILE* 4.1 19.1 - - + -
212B ASN* 3.1 11.7 - - - +
214B ILE* 4.3 15.9 - - + -
142C TYR* 6.3 1.1 - - + -
152C VAL 3.9 0.9 - - - +
153C LEU* 3.4 2.9 - - - +
154C LEU* 2.9 45.7 + - + +
160C LYS* 4.3 1.7 - - - +
161C VAL* 1.3 84.9 - - + +
163C THR* 1.3 63.2 + - - +
164C PHE* 3.6 26.2 - - + -
178C GLY* 4.8 2.5 - - - +
179C VAL* 4.2 20.4 - - + -
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Residues in contact with THR 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B GLY* 3.7 33.9 + - - +
211B ALA* 3.8 0.2 - - - -
212B ASN* 2.7 40.0 + - - +
151C CYS* 4.4 1.1 - - + -
152C VAL 3.4 3.1 - - - +
153C LEU* 3.6 28.0 - - + -
160C LYS* 3.3 31.5 + - - +
162C VAL* 1.3 72.3 + - - +
164C PHE* 1.3 71.4 + - - +
165C CYS* 4.2 10.1 - - - -
194C ASN* 4.8 3.6 - - - +
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Residues in contact with PHE 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B HIS* 3.7 20.4 - - + -
148B SER* 4.1 2.9 - - - -
180B VAL* 3.8 21.3 - - + -
211B ALA* 5.0 0.4 - - - +
212B ASN* 3.3 33.2 - - + -
214B ILE* 3.5 25.8 - - + -
142C TYR* 3.5 16.2 - + - +
151C CYS* 3.4 0.2 - - - -
152C VAL 3.0 23.6 + - - -
162C VAL* 3.6 36.6 - - + -
163C THR* 1.3 76.9 - - - +
165C CYS* 1.3 62.7 + - - +
175C ASN* 2.9 17.8 + - - +
176C SER 3.8 9.4 - - - +
177C GLY* 3.7 22.7 - - - -
178C GLY 4.0 3.1 - - - -
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Residues in contact with CYS 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B SER* 4.7 5.2 + - - -
178B PHE* 4.4 7.1 - - + +
179B GLN* 3.6 24.4 + - - +
180B VAL* 3.6 6.2 + - - +
210B GLY 3.3 24.9 + - - +
211B ALA* 5.2 5.9 - - + +
150C LEU 3.3 2.9 - - - -
151C CYS* 2.1 47.8 - - - -
163C THR* 4.2 3.1 - - - -
164C PHE* 1.3 75.0 - - - +
166C GLY* 1.3 59.0 + - - +
167C HIS* 4.5 13.9 - - + +
175C ASN* 3.8 2.9 - - - -
194C ASN* 4.9 0.4 - - - -
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Residues in contact with GLY 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B PHE 3.9 4.0 - - - -
179B GLN* 4.7 3.8 - - - -
180B VAL* 4.7 4.3 - - - -
146C HIS* 3.4 23.4 + - - -
149C ASN* 3.5 0.5 - - - -
150C LEU 2.8 36.9 + - - -
165C CYS* 1.3 75.6 - - - +
167C HIS* 1.3 66.5 + - - -
173C GLN* 5.8 0.7 - - - -
175C ASN* 3.6 3.1 - - - +
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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