Contacts of the strand formed by residues 124 - 127 (chain B) in PDB entry 1JW9
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 124 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B ARG 3.6 1.2 + - - -
34B VAL* 3.4 13.4 - - + -
35B LEU 3.1 22.5 + - - -
122B HIS* 3.4 4.2 - - - +
123B ASP* 1.3 80.4 - - - +
125B VAL* 1.3 70.3 + - - +
126B LEU* 3.3 33.9 - - + -
147B VAL* 3.8 2.4 - - - +
148B PRO* 3.6 20.2 - - + +
150B VAL* 4.1 10.3 - - + -
208B ALA* 3.9 24.7 - - + +
211B MET* 3.7 31.6 - - + -
212B LEU* 4.0 16.2 - - + -
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Residues in contact with VAL 125 (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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35B LEU* 3.4 22.0 - - + +
37B VAL* 4.1 14.8 - - + -
119B ILE* 4.1 18.6 - - + +
122B HIS* 5.1 1.1 - - + -
124B LEU* 1.3 80.8 - - - +
126B LEU* 1.3 71.7 + - - +
138B LEU* 4.5 8.7 - - + -
142B CYS* 3.7 28.3 - - - -
147B VAL* 4.0 10.5 - - + -
148B PRO 2.9 7.7 + - - +
149B LEU* 3.3 18.5 - - + +
150B VAL 2.8 24.9 + - - -
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B VAL* 3.9 13.7 - - + -
35B LEU 2.8 14.1 + - - +
36B ILE* 4.3 9.0 - - + -
37B VAL* 2.9 34.5 + - - +
46B ALA* 3.6 31.4 - - + -
50B LEU* 4.0 14.1 - - + -
124B LEU* 3.3 27.8 - - + -
125B VAL* 1.3 73.1 - - - +
127B ASP* 1.3 59.4 + - - +
128B CYS* 3.5 12.3 + - - -
150B VAL* 3.4 14.8 - - + +
204B GLN* 3.9 19.5 - - + +
208B ALA* 3.9 11.7 - - + -
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Residues in contact with ASP 127 (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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37B VAL 4.3 0.2 - - - -
126B LEU* 1.3 68.4 - - - +
128B CYS* 1.3 59.0 + - - +
129B THR* 2.7 32.6 + - - +
135B ARG* 1.9 41.1 + - - +
138B LEU* 4.0 15.3 - - + -
149B LEU* 3.8 23.5 - - + +
150B VAL 3.0 7.5 + - - -
151B SER* 2.7 19.6 + - - +
152B GLY 3.3 10.0 + - - +
204B GLN* 3.2 14.0 + - - -
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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