Contacts of the strand formed by residues 168 - 174 (chain A) in PDB entry 3V56
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 TRP 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A LEU* 3.8 37.2 - - + -
150A ILE 3.5 19.1 - - - -
151A ALA* 3.6 11.9 - - - -
152A ASP* 4.2 6.9 - - - +
166A VAL* 3.4 46.5 + - + +
167A PRO* 1.3 74.3 - - - +
169A LEU* 1.3 60.4 + - - +
180A GLU* 5.0 5.4 - - - +
183A ASN* 3.0 46.8 + - - +
261A LEU* 4.1 26.3 + - + +
277A THR* 3.7 10.8 - - + -
278A PHE* 3.6 30.7 - - - -
279A PHE* 3.7 32.6 - + + -
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Residues in contact with LEU 169 (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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149A LEU* 3.4 5.9 - - - -
150A ILE* 2.9 47.4 + - + +
151A ALA 4.7 0.9 - - - +
152A ASP* 4.1 18.4 - - + -
168A TRP* 1.3 73.8 - - - +
170A LEU* 1.3 63.5 + - - +
171A SER 3.3 0.2 + - - -
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Residues in contact with LEU 170 (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 LEU* 3.9 25.8 - - + -
148A GLN 3.8 5.8 - - - +
149A LEU* 4.0 11.1 - - + +
150A ILE* 4.9 2.6 - - - +
169A LEU* 1.3 72.6 - - - +
171A SER* 1.4 60.1 + - - +
172A PHE* 3.3 32.1 - - - +
173A LYS* 4.0 16.2 - - + +
180A GLU* 4.8 12.7 - - + +
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Residues in contact with SER 171 (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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148A GLN* 2.8 53.6 + - - -
150A ILE* 3.8 28.3 - - - +
169A LEU 3.3 3.2 + - - -
170A LEU* 1.4 72.8 - - - +
172A PHE* 1.3 63.7 + - - +
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Residues in contact with PHE 172 (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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146A CYS* 3.5 39.0 - - + -
147A LEU* 3.5 0.2 - - - -
148A GLN* 3.0 58.4 + - + -
170A LEU* 3.3 15.6 - - - +
171A SER* 1.3 86.6 - - - +
173A LYS* 1.3 69.0 + - - +
174A ARG* 4.2 0.4 - - + -
192C TYR* 3.4 31.9 - + + +
250C ILE* 3.5 40.8 - - + -
251C ALA* 4.9 2.7 - - - -
252C LYS* 5.8 2.7 - - + -
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Residues in contact with LYS 173 (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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146A CYS 3.7 5.4 - - - +
147A LEU* 4.0 10.1 - - + +
170A LEU* 4.0 22.0 - - + +
172A PHE* 1.3 77.3 - - - +
174A ARG* 1.3 62.6 + - - +
175A GLY 2.9 25.5 + - - +
176A SER* 4.9 2.7 - - - +
178A LEU 3.4 28.0 - - - +
179A GLU* 4.2 17.7 - - - -
180A GLU 5.5 0.7 - - - +
192C TYR* 4.7 4.7 + - - -
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Residues in contact with ARG 174 (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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143A THR* 3.6 21.2 + - - +
144A GLN* 2.8 31.7 + - - +
145A ASP* 3.3 6.9 - - - +
146A CYS* 2.8 55.4 + - - +
172A PHE* 4.2 7.0 - - + -
173A LYS* 1.3 75.9 - - - +
175A GLY* 1.3 64.5 + - - +
178A LEU* 5.4 2.3 + - - +
192C TYR* 3.3 43.6 - - + +
284C LEU* 4.3 13.3 + - - +
285C LEU* 2.9 38.2 + - - -
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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