Contacts of the strand formed by residues 168 - 172 (chain A) in PDB entry 3VZC
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 SER 168 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LEU* 5.2 0.2 - - - -
165A SER* 3.3 9.3 + - - -
167A LEU* 1.3 93.1 - - - +
169A LEU* 1.3 60.9 + - - +
170A ALA* 4.2 3.4 - - - +
261A LEU* 4.1 11.4 - - - -
262A ALA 3.0 12.6 - - - -
263A LEU* 4.1 13.5 - - - -
264A LEU* 4.9 1.1 - - - -
268A LEU* 4.8 7.3 - - - +
339A ALA 4.3 1.1 + - - -
340A VAL* 3.6 2.1 - - - -
341A ASP* 2.8 41.0 + - - +
342A GLY 4.6 2.8 + - - -
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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
----------------------------------------------------------
153A LEU* 4.6 10.6 - - + +
155A LEU* 4.3 9.6 - - + -
168A SER* 1.3 72.5 - - - +
170A ALA* 1.3 65.0 + - - +
171A TRP 5.0 0.2 - - - +
260A VAL* 4.1 3.2 - - + +
261A LEU* 3.6 2.2 - - - +
262A ALA* 2.8 45.8 + - + +
327A PHE* 3.9 29.6 - - + -
329A LEU* 4.7 6.5 - - + -
338A PHE* 3.7 39.7 - - + -
339A ALA 3.4 3.6 - - - -
340A VAL* 3.9 24.9 - - + -
345A MET* 4.8 1.6 - - + -
350A VAL* 4.1 18.2 - - + -
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Residues in contact with ALA 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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168A SER* 5.4 3.4 - - - +
169A LEU* 1.3 77.5 - - - +
171A TRP* 1.3 60.8 + - - +
174A ILE* 3.7 33.0 - - + -
175A ALA* 3.8 2.9 - - - +
178A ASP* 5.3 0.7 - - - +
260A VAL 3.4 7.2 - - - +
261A LEU* 4.2 11.0 - - + +
268A LEU* 5.9 0.2 - - + -
338A PHE* 3.3 7.6 - - - +
339A ALA* 3.0 40.7 + - + +
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Residues in contact with TRP 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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169A LEU* 5.0 0.4 - - + -
170A ALA* 1.3 77.1 - - - +
172A GLY* 1.3 69.7 + - - +
174A ILE* 4.6 1.4 + - - +
175A ALA* 4.0 5.4 - - - -
206A TYR* 3.5 32.8 - - + +
207A ARG 3.8 14.1 - - - -
208A GLY* 3.8 12.6 - - - -
257A PHE* 3.9 26.7 - + + -
259A LEU* 3.3 7.2 - - - +
260A VAL* 2.9 51.9 + - + +
329A LEU* 3.7 29.4 - - + -
331A PRO* 3.8 34.5 - - + +
336A GLY* 4.2 6.9 - - - -
337A VAL 3.3 22.7 + - - +
338A PHE* 3.7 25.4 - + + -
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Residues in contact with GLY 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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171A TRP* 1.3 85.4 - - - +
173A PHE* 1.3 66.6 + - - -
175A ALA* 2.9 5.7 + - - +
176A ASP* 2.8 24.0 + - - +
206A TYR* 3.3 38.8 - - - -
258A VAL 3.6 1.3 - - - -
259A LEU* 4.5 0.4 - - - -
337A VAL 4.2 0.8 + - - -
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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