Contacts of the strand formed by residues 130 - 135 (chain A) in PDB entry 6WNX
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 VAL 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A CYS* 3.6 31.6 - - + -
129A GLY* 1.3 74.4 - - - +
131A TYR* 1.3 56.7 + - - +
132A CYS 3.6 15.7 - - - +
142A SER* 4.0 16.4 - - - -
143A GLY 3.4 8.7 - - - +
144A LEU* 4.1 9.2 - - + -
383A PHE* 3.3 15.3 - - - +
395A SER* 2.8 46.2 + - - +
396A SER 3.1 15.4 + - - +
399A ASP* 4.3 8.7 - - - +
400A THR 4.4 2.2 - - - +
401A ILE* 4.3 3.1 - - + -
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Residues in contact with TYR 131 (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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129A GLY 5.1 1.3 - - - -
130A VAL* 1.3 73.6 - - - +
132A CYS* 1.3 60.1 + - - +
143A GLY 2.8 5.9 + - - -
145A ARG* 3.1 38.5 + - + -
169A SER* 3.7 12.3 - - - -
170A VAL 3.4 19.3 - - - +
171A LEU* 3.6 29.1 - - + +
334A ARG* 3.9 14.8 + - - +
383A PHE* 3.4 54.9 - + - +
384A ARG* 3.7 2.8 - - - +
32C ASP* 3.5 26.2 + - - -
33C SEP 2.8 46.3 + - - -
34C GLY 4.0 1.3 - - - -
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Residues in contact with CYS 132 (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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130A VAL* 3.4 8.1 - - - +
131A TYR* 1.3 78.3 - - - +
133A LEU* 1.3 65.9 + - - +
142A SER* 3.4 2.1 - - - -
143A GLY* 3.1 42.7 + - - -
170A VAL* 3.7 14.1 - - - -
171A LEU 3.5 9.9 - - - +
172A CYS* 3.7 22.9 - - - -
173A LEU* 3.5 20.6 - - + +
384A ARG* 3.8 17.3 - - + +
395A SER* 4.2 1.1 - - - -
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Residues in contact with LEU 133 (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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132A CYS* 1.3 78.7 - - - +
134A GLN* 1.3 74.5 + - - +
135A TYR* 4.5 2.5 - - + -
140A ILE* 4.6 6.5 - - + -
141A ILE 3.2 13.9 - - - +
142A SER* 4.2 6.7 - - - +
173A LEU* 4.3 7.8 - - - +
384A ARG* 3.6 29.5 + - + +
385A LEU 4.8 0.2 - - - -
386A GLN* 4.1 18.1 - - + +
393A ILE* 3.9 32.5 - - + +
394A SER 3.7 6.7 - - - -
395A SER* 3.5 40.6 - - - +
401A ILE* 5.0 3.1 - - + -
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Residues in contact with GLN 134 (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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133A LEU* 1.3 79.3 - - - +
135A TYR* 1.3 65.6 + - - +
140A ILE* 3.5 1.9 - - - +
141A ILE 2.8 32.4 + - - +
173A LEU* 4.0 8.0 - - + +
174A GLN* 3.1 19.7 - - - +
175A TYR* 2.8 77.5 + - + -
386A GLN* 3.2 14.8 - - - +
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Residues in contact with TYR 135 (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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133A LEU* 4.5 1.6 - - + -
134A GLN* 1.3 78.7 + - - +
136A ASP* 1.3 73.7 + - - +
139A LYS 3.2 13.0 - - - +
140A ILE* 3.8 18.2 - - + -
154A LYS* 3.9 6.1 - - - -
175A TYR* 3.1 10.0 + - - -
386A GLN* 3.1 72.2 + - + +
387A PHE* 3.5 12.1 - - - -
388A ASP* 2.9 30.9 + - + +
391A GLN* 3.3 30.0 - - - +
393A ILE* 3.4 28.5 - - + -
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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