Contacts of the strand formed by residues 118 - 123 (chain B) in PDB entry 2J25
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 ILE 118 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LYS* 4.1 17.0 - - + +
80B GLY* 3.5 8.3 - - - +
81B PHE* 2.9 34.0 + - - +
82B GLY* 3.0 21.1 - - - +
83B GLY 3.4 2.6 + - - -
109B PHE* 4.4 3.3 - - - -
117B ASN* 1.3 88.6 - - - +
119B ILE* 1.3 75.3 + - - +
172B VAL* 3.9 0.2 - - - +
173B SER* 3.3 18.2 - - - +
175B LEU* 4.8 9.6 - - + -
228B TRP* 4.5 3.1 - - + -
337B PHE* 4.0 26.9 - - + -
379B THR* 3.9 25.1 - - + +
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Residues in contact with ILE 119 (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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83B GLY 3.3 7.6 - - - +
85B MET* 3.7 24.0 - - + +
109B PHE* 3.5 36.1 - - + -
118B ILE* 1.3 82.8 - - - +
120B ARG* 1.3 74.6 + - - +
121B VAL* 3.7 8.4 + - + +
161B ILE* 4.4 12.8 - - + -
164B ALA* 3.9 15.3 - - + -
165B LEU* 4.4 4.3 - - + -
172B VAL* 4.1 12.3 - - + +
173B SER 3.0 7.9 + - - -
174B LEU* 3.5 18.6 - - + +
175B LEU 3.0 22.5 + - - +
383B LEU* 5.1 2.0 - - + -
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Residues in contact with ARG 120 (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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83B GLY 2.9 8.8 + - - +
84B ALA* 3.3 18.2 - - + +
85B MET 2.7 30.8 + - - -
118B ILE 4.2 0.2 - - - -
119B ILE* 1.3 74.0 - - - +
121B VAL* 1.3 67.6 + - - +
122B PRO* 4.0 1.6 - - + +
175B LEU* 3.1 24.7 - - + +
177B SER* 2.9 24.8 + - - +
179B TRP* 3.6 15.9 - - + -
234B ASN* 3.0 19.2 + - - +
282B ASP* 2.9 33.2 + - - -
311B HIS* 3.8 1.0 + - - -
339B SER* 3.4 31.6 + - - -
340B GLU* 3.0 26.9 + - - +
379B THR* 4.2 12.1 - - + +
381B TRP* 4.0 6.7 - - - -
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B MET* 4.7 2.0 - - + +
119B ILE* 4.0 11.0 - - + +
120B ARG* 1.3 81.4 - - - +
122B PRO* 1.3 70.1 - - - +
123B MET 3.4 0.3 + - - -
157B LYS* 3.5 30.1 - - - -
161B ILE* 3.7 24.9 - - + -
174B LEU* 4.9 2.0 - - + -
175B LEU 2.6 10.7 + - - +
176B ALA* 3.2 4.3 - - + +
177B SER 2.9 23.0 + - - -
216B PHE* 4.6 2.7 - - + -
220B TYR* 3.7 18.8 - - + +
227B PHE* 3.8 27.6 - - + -
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Residues in contact with PRO 122 (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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84B ALA* 5.2 0.7 - - + -
85B MET 3.4 24.2 - - - +
86B THR* 4.0 25.1 - - + -
87B ASP* 5.2 1.6 - - - +
120B ARG* 4.0 3.6 - - + +
121B VAL* 1.3 86.0 - - + +
123B MET* 1.3 59.5 + - - +
124B ALA 3.3 14.9 + - - +
126B CYS* 4.6 10.3 - - + -
135B TYR* 3.7 1.0 + - - -
157B LYS* 2.9 29.2 + - - +
177B SER 3.2 7.0 - - - +
179B TRP* 3.5 30.3 - - + -
381B TRP* 4.7 1.3 - - + -
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Residues in contact with MET 123 (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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122B PRO* 1.3 67.5 - - - +
124B ALA* 1.3 71.3 + - - +
125B SER 4.7 1.4 - - - +
135B TYR* 3.4 17.7 - - + -
176B ALA* 3.8 16.2 - - + -
177B SER 2.7 15.0 + - - +
178B PRO* 3.4 44.8 - - + +
179B TRP* 4.4 4.9 + - - -
180B THR 4.7 4.5 + - - +
212B TYR* 4.0 17.6 + - + -
213B PHE* 3.9 33.7 - - + -
216B PHE* 3.7 48.2 - - + -
230B VAL* 5.4 0.9 - - - -
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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