Contacts of the strand formed by residues 161 - 166 (chain C) in PDB entry 4JHN
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 LEU 161 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C ALA* 4.3 1.6 - - + -
154C ALA 3.7 10.5 - - - +
155C LEU* 4.2 7.9 - - + -
159C GLY 3.7 1.2 + - - -
160C ARG* 1.3 74.6 - - - +
162C PHE* 1.3 72.4 + - - +
163C MET* 4.2 7.6 - - + -
185C GLN* 3.3 11.2 - - - +
186C VAL* 2.8 50.6 + - + +
192C VAL* 4.1 13.9 - - + +
195C ILE* 3.3 52.3 - - + -
204C PHE* 3.6 31.0 - - + -
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Residues in contact with PHE 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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135C PHE* 3.7 28.0 - + - -
136C PHE* 3.9 29.2 - + + -
140C HIS* 4.0 29.8 - + + -
153C ALA* 3.2 4.2 - - - +
154C ALA 2.8 41.1 + - - +
156C THR* 5.2 4.3 - - + -
160C ARG* 3.8 39.0 - - + -
161C LEU* 1.3 73.9 - - - +
163C MET* 1.3 65.5 + - - +
164C TRP* 3.6 4.6 - - + -
183C PRO* 4.3 3.6 - - + -
184C GLN 3.4 4.9 - - - +
185C GLN* 3.7 35.9 - - + -
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Residues in contact with MET 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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152C SER 3.2 6.5 - - - +
153C ALA* 3.9 7.0 - - + -
161C LEU* 4.2 8.7 - - + -
162C PHE* 1.3 80.1 - - - +
164C TRP* 1.3 64.1 + - - +
171C GLN 3.9 0.9 - - - +
172C ILE* 3.8 33.2 - - + +
174C LEU* 4.5 2.1 - - + +
180C VAL* 4.1 2.4 - - - +
184C GLN* 2.9 33.8 + - - +
186C VAL* 3.8 17.9 - - + -
195C ILE* 3.8 20.6 - - + -
197C CYS* 3.6 30.3 - - - -
202C SER* 3.8 19.3 - - - +
214C PHE* 3.8 20.4 - - - -
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Residues in contact with TRP 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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100C LEU* 4.0 11.7 - - + -
108C VAL* 5.4 2.9 - - + -
117C GLY 3.4 7.2 - - - -
118C GLN 2.8 29.4 + - - -
119C LEU 3.5 1.2 - - - -
120C GLY* 3.3 30.6 - - - +
133C ILE* 3.9 19.5 - - + -
136C PHE* 3.7 32.1 - + - -
151C THR* 3.6 3.1 - - - -
152C SER* 3.0 46.5 + - - +
153C ALA 4.1 4.9 - - - -
154C ALA* 3.8 17.0 - - + -
162C PHE 3.6 17.0 - - - -
163C MET* 1.3 84.8 - - - +
165C GLY* 1.3 59.5 + - - +
172C ILE* 3.6 9.3 - - - +
180C VAL* 3.6 12.3 - - + +
182C VAL 3.7 19.3 - - - +
183C PRO* 3.6 17.7 - - + -
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Residues in contact with GLY 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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116C GLU 3.4 19.7 - - - -
118C GLN* 3.8 11.0 - - - -
150C ASN 3.4 9.0 - - - -
164C TRP* 1.3 75.9 - - - +
166C ASP* 1.3 64.7 + - - -
172C ILE* 3.4 4.2 - - - +
179C ASN* 3.2 2.4 - - - -
180C VAL 2.8 35.7 + - - -
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Residues in contact with ASP 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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116C GLU* 3.7 34.6 - - + +
149C SER 4.5 2.6 - - - +
150C ASN* 2.9 24.9 + - + +
151C THR* 3.5 19.9 - - + +
165C GLY* 1.3 72.0 - - - -
167C ASN* 1.3 68.0 + - - +
168C SER* 3.0 30.9 + - - -
171C GLN* 3.5 18.8 + - - +
172C ILE* 3.6 10.1 - - - +
178C SER 3.4 4.2 - - - +
179C ASN* 4.1 2.5 - - - -
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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