Contacts of the strand formed by residues 170 - 175 (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 LYS 170 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B GLN* 3.7 20.4 + - - +
168B GLY 4.3 4.0 - - - +
169B ASP* 1.3 74.2 - - - +
171B ILE* 1.3 62.9 + - - +
197B TYR* 5.1 0.2 - - - -
198B GLU* 3.3 43.7 - - + +
219B ASP* 4.2 2.9 - - - +
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Residues in contact with ILE 171 (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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107B PHE* 3.6 31.9 - - + -
111B GLN* 4.8 1.8 - - - +
114B ALA* 4.2 14.1 - - + -
118B LEU* 4.9 5.6 - - + -
170B LYS* 1.3 77.1 - - - +
172B ASN* 1.3 58.6 + - - +
173B LEU* 4.0 24.5 - - + -
192B LEU* 4.6 12.8 - - + -
197B TYR* 4.0 18.8 - - + -
198B GLU 2.8 18.2 + - - +
199B VAL* 3.5 25.4 - - + +
200B THR* 2.8 34.8 + - - +
219B ASP* 3.4 11.7 - - + +
220B ALA* 5.2 0.2 - - + -
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Residues in contact with ASN 172 (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* 1.3 73.6 - - - +
173B LEU* 1.3 65.8 + - - +
174B ALA 3.7 1.5 + - - +
200B THR* 3.5 17.0 + - - +
202B THR* 2.9 35.9 + - - +
217B SER 3.7 14.7 - - - +
218B ALA* 4.3 9.2 - - - +
219B ASP* 2.7 42.4 + - - +
220B ALA 3.2 8.5 + - - +
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Residues in contact with LEU 173 (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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118B LEU* 4.4 11.9 - - + -
171B ILE* 4.2 19.1 - - + -
172B ASN* 1.3 74.0 - - - +
174B ALA* 1.3 57.7 + - - +
175B TYR* 3.8 1.2 + - - -
185B THR* 4.1 12.8 - - + +
188B ILE* 4.0 13.9 - - + -
189B GLY* 4.1 8.3 - - - -
192B LEU* 4.0 19.7 - - + -
199B VAL* 4.1 8.1 - - + -
200B THR 2.7 11.1 + - - +
201B LEU* 3.1 32.5 - - + +
202B THR 2.7 28.6 + - - -
220B ALA* 3.3 31.9 - - + +
221B SER* 5.1 1.1 - - - +
222B LEU* 5.1 4.5 - - + -
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Residues in contact with ALA 174 (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* 3.7 2.4 + - - +
173B LEU* 1.3 71.7 - - - +
175B TYR* 1.3 61.3 + - - +
185B THR* 4.8 2.6 - - - +
202B THR* 3.3 13.9 - - + +
204B VAL* 4.3 7.6 - - + -
209B MET* 4.3 19.7 - - + +
212B ALA* 5.1 2.5 - - + -
213B ILE* 4.7 2.5 - - + -
218B ALA* 3.8 23.8 - - + -
220B ALA 2.7 11.0 + - - +
221B SER* 3.0 32.7 + - - -
222B LEU 4.1 2.3 + - - -
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Residues in contact with TYR 175 (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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174B ALA* 1.3 75.1 - - - +
176B VAL* 1.3 76.5 + - - +
177B ALA* 4.1 7.8 + - + -
181B GLU 4.4 6.5 - - - +
182B ILE* 4.6 15.7 - - + -
185B THR* 3.3 33.7 - - + +
186B ASN* 5.7 4.0 - - - -
201B LEU* 3.6 35.8 + - + +
202B THR 3.0 13.4 + - - -
203B GLN* 3.5 51.4 + - + +
204B VAL* 3.1 26.6 + - - +
209B MET* 4.9 0.2 - - - -
223B SER* 3.7 6.3 - - - +
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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