Contacts of the strand formed by residues 198 - 203 (chain B) in PDB entry 2B4M
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 GLU 198 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168B GLY* 3.6 20.3 - - - +
169B ASP 2.6 10.9 + - - +
170B LYS* 3.3 41.4 - - - +
171B ILE 2.8 27.8 + - - +
197B TYR* 1.3 69.0 - - - +
199B VAL* 1.3 62.3 + - - +
200B THR* 3.9 8.5 + - - +
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Residues in contact with VAL 199 (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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171B ILE* 3.5 16.2 - - + +
173B LEU* 4.1 23.1 - - + -
189B GLY* 3.8 11.7 - - - +
192B LEU* 3.7 24.0 - - + -
193B GLU* 3.6 37.1 + - + +
197B TYR* 3.5 9.3 + - + +
198B GLU* 1.3 75.8 - - - +
200B THR* 1.3 73.5 + - - +
201B LEU* 4.3 7.3 + - + +
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Residues in contact with THR 200 (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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171B ILE 2.8 11.9 + - - +
172B ASN* 4.2 11.4 - - - +
173B LEU* 2.7 34.8 + - - +
198B GLU* 3.9 9.6 + - - +
199B VAL* 1.3 75.4 + - - +
201B LEU* 1.3 63.5 + - - +
202B THR* 3.8 19.1 - - - +
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Residues in contact with LEU 201 (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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173B LEU* 3.1 27.4 - - + -
175B TYR* 3.6 22.2 + - + -
185B THR* 3.6 33.4 - - + +
186B ASN* 4.3 26.9 - - - +
189B GLY* 4.7 3.8 - - - -
199B VAL* 4.3 10.3 + - + +
200B THR* 1.3 79.4 - - - +
202B THR* 1.3 61.1 + - - +
203B GLN 3.9 1.9 + - - -
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Residues in contact with THR 202 (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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172B ASN* 2.9 29.4 + - - +
173B LEU 2.7 9.8 + - - -
174B ALA* 3.3 9.4 - - + -
175B TYR* 3.0 25.2 + - - +
200B THR* 3.8 8.8 - - - +
201B LEU* 1.3 71.4 - - - +
203B GLN* 1.3 71.6 + - - +
204B VAL* 3.8 12.8 + - + +
218B ALA* 5.8 1.1 - - - -
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Residues in contact with GLN 203 (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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175B TYR* 3.5 43.2 + - + +
177B ALA* 3.1 29.4 - - + +
201B LEU 3.9 1.4 + - - -
202B THR* 1.3 75.2 - - - +
204B VAL* 1.3 74.5 + - - +
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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