Contacts of the strand formed by residues 174 - 178 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A LEU* 5.8 1.3 - - + -
132A VAL* 4.1 24.5 - - + -
148A LEU* 3.2 24.2 - - + +
150A LEU* 4.2 16.2 - - + -
164A LEU* 3.8 36.6 - - + -
167A TYR* 4.2 22.9 - - + -
172A VAL* 3.5 15.4 + - + +
173A LYS* 1.3 76.1 - - - +
175A TYR* 1.3 71.7 + - - +
176A THR* 5.1 0.2 - - + -
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Residues in contact with TYR 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A PRO* 3.6 18.7 - - + +
148A LEU 2.9 14.0 + - - +
149A VAL* 3.3 9.9 - - + +
150A LEU* 2.8 27.0 + - - +
173A LYS* 3.3 47.3 - - + +
174A ILE* 1.3 77.0 - - - +
176A THR* 1.3 65.0 + - - +
224A LEU* 4.0 30.5 - - + -
227A THR* 5.8 5.4 - - + -
228A PHE* 3.7 24.8 - + - -
231A GLU* 4.8 8.0 + - - -
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Residues in contact with THR 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A LEU* 3.4 20.2 - - + -
152A ASN* 3.7 21.5 - - - +
157A ASP* 4.0 13.5 - - - +
160A THR* 4.8 3.6 - - - +
161A LYS* 3.8 22.7 - - + +
164A LEU* 4.3 19.7 - - + -
174A ILE* 5.1 0.4 - - + -
175A TYR* 1.3 77.9 - - - +
177A PHE* 1.3 66.6 + - - +
178A ASN* 5.7 0.2 - - - -
224A LEU* 4.1 7.5 - - - +
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Residues in contact with PHE 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A VAL* 4.6 5.4 - - + -
149A VAL* 3.7 27.6 - - + -
150A LEU 3.2 8.9 + - - -
151A MET* 3.2 48.3 - - + -
152A ASN* 3.0 26.5 + - - +
176A THR* 1.3 79.0 - - - +
178A ASN* 1.3 71.0 + - - +
179A GLN 3.9 0.3 + - - -
215A ILE* 4.3 2.7 - - + -
218A SER* 3.3 28.7 - - - -
219A PHE* 3.4 36.3 - + + -
222A SER* 4.1 9.6 - - - -
224A LEU* 3.8 15.0 - - + -
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Residues in contact with ASN 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A LYS* 4.8 5.5 + - - -
152A ASN 3.3 3.1 + - - -
153A SER 3.8 11.9 + - - -
154A PHE* 4.3 8.7 - - - +
157A ASP* 2.7 45.6 + - - +
161A LYS* 4.7 2.4 + - - -
176A THR 5.5 0.2 - - - -
177A PHE* 1.3 81.7 - - - +
179A GLN* 1.3 70.2 + - - +
218A SER* 3.6 18.5 - - - +
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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