Contacts of the strand formed by residues 168 - 174 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149B LEU* 3.8 32.3 - - + -
150B ILE 3.5 22.2 - - - -
151B ALA* 3.6 17.3 - - - -
152B ASP* 4.3 7.0 - - - +
166B VAL* 3.4 44.5 + - + +
167B PRO* 1.3 73.8 - - - +
169B LEU* 1.3 60.9 + - - +
180B GLU* 5.0 5.7 - - - +
183B ASN* 3.0 50.0 + - - +
261B LEU* 4.1 27.3 + - + +
277B THR* 3.7 11.7 - - + -
278B PHE* 3.6 25.1 - - - -
279B PHE* 3.7 31.6 - - + -
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Residues in contact with LEU 169 (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 LEU* 3.4 6.7 - - - -
150B ILE* 2.9 47.5 + - + +
151B ALA 4.6 3.1 - - - +
152B ASP* 3.7 36.8 - - + +
153B SER 5.3 0.2 - - - +
154B GLU* 5.3 4.9 - - - +
168B TRP* 1.3 73.2 - - - +
170B LEU* 1.3 73.9 + - - +
171B SER 3.2 0.2 + - - -
180B GLU* 6.0 0.2 - - - -
219F VAL* 5.0 7.2 - - + -
225F SER* 4.6 20.4 - - - +
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Residues in contact with LEU 170 (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 LEU* 3.9 25.1 - - + -
148B GLN 3.8 6.1 - - - +
149B LEU* 4.0 11.5 - - + +
150B ILE* 5.1 0.3 - - - +
169B LEU* 1.3 85.3 - - - +
171B SER* 1.3 61.9 - - - +
172B PHE* 3.3 27.1 - - - +
173B LYS* 3.9 10.5 - - + +
180B GLU* 4.8 14.2 - - + +
217F VAL* 4.0 17.8 - - + +
218F HIS* 3.9 27.8 - - + +
219F VAL* 4.1 8.8 + - - +
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Residues in contact with SER 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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148B GLN* 2.8 42.6 + - - -
150B ILE* 3.8 24.2 - - - +
169B LEU 3.2 3.4 + - - -
170B LEU* 1.3 72.0 - - - +
172B PHE* 1.3 61.0 + - - +
218F HIS* 2.9 12.0 - - - +
219F VAL 2.5 47.3 + - - +
220F PHE* 3.7 9.4 - - - -
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Residues in contact with PHE 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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192A TYR* 3.3 26.5 - + + -
250A ILE* 3.4 45.8 - - + -
146B CYS* 3.6 36.1 - - + -
147B LEU* 3.5 0.2 - - - -
148B GLN* 3.0 51.7 + - + -
170B LEU* 3.3 10.9 - - - +
171B SER* 1.3 81.4 - - - +
173B LYS* 1.3 68.2 + - - +
174B ARG* 4.1 2.0 - - + -
218F HIS* 3.4 26.2 - - + +
220F PHE* 3.5 25.6 - + + -
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Residues in contact with LYS 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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192A TYR* 4.8 1.2 + - - -
146B CYS 3.6 6.5 - - - +
147B LEU* 4.0 10.3 - - + +
170B LEU* 3.9 18.6 - - + -
172B PHE* 1.3 76.6 - - - +
174B ARG* 1.3 63.2 + - - +
175B GLY 4.2 11.7 - - - +
178B LEU 3.8 25.1 - - - +
179B GLU* 4.7 10.5 - - + -
180B GLU 5.5 1.1 - - - +
218F HIS* 3.6 20.6 + - - +
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Residues in contact with ARG 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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192A TYR* 3.8 36.1 - - + +
284A LEU* 3.9 19.0 + - - +
285A LEU* 2.6 45.4 + - - -
143B THR* 3.5 18.7 - - - +
144B GLN 2.8 26.5 + - - +
145B ASP* 3.2 5.6 - - - +
146B CYS* 2.8 52.1 + - - +
172B PHE* 4.1 6.5 - - + -
173B LYS* 1.3 76.6 - - - +
175B GLY* 1.3 63.3 + - - +
178B LEU* 5.5 1.9 + - - +
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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