Contacts of the strand formed by residues 174 - 178 (chain B) in PDB entry 3R2W
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 174 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128B LEU* 6.3 0.7 - - + -
132B VAL* 4.6 9.0 - - + -
148B LEU* 3.3 35.2 - - + +
150B LEU* 4.9 12.1 - - + -
164B LEU* 4.5 33.2 - - + +
167B TYR* 4.2 31.0 - - + +
172B VAL* 3.8 24.0 - - + +
173B LYS* 1.3 71.9 - - - +
175B TYR* 1.3 63.6 + - - +
176B THR* 4.4 0.8 + - - -
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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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147B PRO* 4.0 10.8 - - + -
148B LEU 2.7 15.8 + - - -
149B VAL* 3.0 20.6 - - + +
150B LEU* 2.8 26.0 + - - +
173B LYS* 3.7 29.5 - - + +
174B ILE* 1.3 79.8 - - - +
176B THR* 1.3 64.5 + - - +
224B LEU* 4.3 22.4 - - + -
227B THR* 6.2 2.0 - - + -
228B PHE* 3.9 32.2 - + - -
231B GLU* 4.7 9.4 + - - -
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Residues in contact with THR 176 (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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149B VAL* 5.1 0.2 - - - -
150B LEU* 3.5 21.8 - - + -
152B ASN* 3.8 24.2 - - - +
157B ASP* 4.6 11.4 + - - +
160B THR* 5.3 2.7 - - - +
161B LYS* 5.4 4.2 - - + +
164B LEU* 3.9 27.7 - - + +
174B ILE 4.4 0.4 + - - -
175B TYR* 1.3 79.1 - - - +
177B PHE* 1.3 69.2 + - - +
224B LEU* 4.7 4.9 - - - +
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Residues in contact with PHE 177 (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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100B VAL* 5.2 2.5 - - + -
149B VAL* 3.8 22.4 - - + -
150B LEU 3.2 7.4 + - - -
151B MET* 3.2 43.4 - - + -
152B ASN* 3.1 31.4 + - - +
157B ASP* 4.2 2.5 - - - -
176B THR* 1.3 79.4 - - - +
178B ASN* 1.3 68.2 + - - +
215B ILE* 4.1 10.1 - - + -
218B SER* 3.4 43.5 - - - -
219B PHE* 3.7 18.2 - + - -
222B SER* 4.2 19.7 - - - -
224B LEU* 4.6 4.5 - - + -
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Residues in contact with ASN 178 (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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152B ASN* 3.4 1.7 - - - +
153B SER* 3.3 28.2 - - - -
154B PHE* 3.5 5.9 + - - -
157B ASP* 2.7 37.2 + - - +
177B PHE* 1.3 87.1 - - - +
179B GLN* 1.3 69.1 + - - +
218B SER* 4.1 7.8 - - - +
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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