Contacts of the strand formed by residues 179 - 185 (chain B) 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 ASN 179 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ASN 5.0 1.0 + - - -
116B GLU* 3.1 42.6 + - - +
117B GLY* 4.4 1.6 - - - +
124B THR* 4.9 8.7 - - - +
165B GLY 3.3 15.3 - - - +
166B ASP* 4.2 0.4 - - - -
167B ASN* 4.0 3.4 - - - +
177B VAL* 3.4 9.0 - - - +
178B SER* 1.3 95.6 + - - +
180B VAL* 1.3 74.2 + - - +
181B CYS* 4.8 3.4 - - - +
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Residues in contact with VAL 180 (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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116B GLU 3.7 2.8 - - - +
117B GLY 3.4 4.5 - - - +
163B MET 4.3 3.8 - - - +
164B TRP* 3.7 10.7 - - + +
165B GLY* 2.8 36.9 + - - +
167B ASN* 5.9 0.2 - - + -
172B ILE* 4.4 4.3 - - + -
174B LEU* 3.8 18.8 - - + -
177B VAL* 3.8 14.6 - - + -
179B ASN* 1.3 82.6 - - - +
181B CYS* 1.3 61.0 + - - +
182B VAL* 2.8 31.9 - - + +
184B GLN* 3.6 28.7 - - + +
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Residues in contact with CYS 181 (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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117B GLY* 3.5 24.9 - - - -
120B GLY* 3.1 15.4 - - - -
121B LEU 5.3 0.2 - - - +
122B GLY* 2.9 48.6 + - - -
123B ASP* 3.8 14.4 - - - +
124B THR* 5.1 3.6 - - + -
164B TRP* 4.9 0.2 - - - -
179B ASN* 4.8 5.1 - - - +
180B VAL* 1.3 73.8 - - - +
182B VAL* 1.3 61.7 + - - +
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Residues in contact with VAL 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLY 4.2 2.5 - - - +
121B LEU 5.2 0.2 - - - -
122B GLY* 4.0 16.8 - - - +
135B PHE* 4.5 12.3 - - + -
164B TRP* 4.1 2.5 - - - -
180B VAL* 2.8 22.1 - - + +
181B CYS* 1.3 90.1 - - - +
183B PRO* 1.4 89.0 - - + +
184B GLN* 4.1 1.4 + - - +
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Residues in contact with PRO 183 (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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120B GLY* 3.7 16.8 - - - +
133B ILE* 3.8 8.7 - - + -
135B PHE* 3.7 45.8 - - + -
136B PHE* 3.6 27.4 - - + -
162B PHE* 4.3 2.9 - - + -
163B MET 3.9 0.9 - - - +
164B TRP* 3.7 29.8 - - + -
182B VAL* 1.4 97.4 - - + +
184B GLN* 1.3 59.4 + - - +
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Residues in contact with GLN 184 (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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135B PHE* 5.5 0.2 - - - -
162B PHE* 3.3 5.5 - - - -
163B MET 2.8 36.3 + - - +
174B LEU* 3.7 26.9 - - + +
177B VAL* 5.7 5.0 - - - +
180B VAL* 3.6 26.7 - - - +
182B VAL 4.1 3.1 + - - +
183B PRO* 1.3 75.6 - - - +
185B GLN* 1.3 70.2 + - - +
186B VAL* 4.0 2.1 - - - +
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Residues in contact with GLN 185 (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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160B ARG* 3.9 29.7 - - - +
161B LEU 3.3 12.9 - - - +
162B PHE* 3.7 24.4 - - + -
174B LEU* 3.9 10.7 - - - +
184B GLN* 1.3 79.1 - - - +
186B VAL* 1.3 70.9 + - - +
187B THR* 4.1 25.0 + - + +
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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