Contacts of the strand formed by residues 165 - 169 (chain C) in PDB entry 4WCX
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 ARG 165 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C LYS 3.3 3.8 + - - -
129C ARG* 3.3 41.6 - - + +
130C LEU 3.1 24.4 + - - +
154C TYR* 4.4 1.8 - - - -
163C ILE* 3.6 2.8 - - - +
164C ARG* 1.3 80.2 - - - +
166C VAL* 1.3 62.8 + - - +
167C ASN* 3.1 20.8 + - - +
187C GLY* 3.4 21.4 - - - -
188C THR* 2.8 25.0 + - - -
230C ASP* 3.0 26.9 + - - -
265C HIS* 3.9 12.7 + - - -
381C THR* 4.1 14.8 - - + -
383C CYS* 5.2 4.4 - - - +
384C TYR* 3.6 39.0 - - + +
388C ARG 5.5 1.0 + - - -
389C THR* 5.2 2.0 - - - +
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Residues in contact with VAL 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C LEU* 3.5 6.5 - - + +
132C VAL* 3.8 22.2 - - + -
150C ILE* 4.3 18.8 - - + -
153C ILE* 3.7 30.1 - - + -
154C TYR* 3.4 39.4 + - + +
163C ILE* 3.7 7.0 - - + -
165C ARG* 1.3 75.2 - - - +
167C ASN* 1.3 70.7 + - - +
168C VAL* 4.4 1.8 - - + -
186C ILE* 3.7 6.2 - - - +
187C GLY 2.8 27.9 + - - -
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Residues in contact with ASN 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C PHE* 5.7 6.5 - - - +
129C ARG* 5.0 7.2 - - - +
130C LEU 2.9 14.8 + - - +
131C ALA* 4.1 13.4 - - + +
132C VAL 2.8 24.7 + - - -
165C ARG* 3.1 22.6 + - - +
166C VAL* 1.3 77.7 - - - +
168C VAL* 1.3 63.9 + - - +
188C THR* 2.8 45.4 + - - +
190C VAL* 4.6 9.6 - - + +
309C ILE* 6.0 1.6 - - - +
329C GLN* 4.6 15.6 - - - +
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Residues in contact with VAL 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C VAL* 3.6 8.7 - - + +
146C ILE* 4.3 8.5 - - + -
150C ILE* 3.6 31.2 - - + -
166C VAL* 4.4 3.8 - - + -
167C ASN* 1.3 79.9 - - - +
169C ASN* 1.3 62.0 + - - +
170C ILE* 3.8 33.7 - - + -
181C LEU* 4.3 11.4 - - + -
186C ILE* 3.8 24.9 - - + +
188C THR 3.0 8.5 + - - +
189C TYR* 3.4 7.2 - - + -
190C VAL* 2.9 26.1 + - - -
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Residues in contact with ASN 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C ALA* 5.5 3.3 - - + -
132C VAL 2.8 14.3 + - - +
133C GLU* 3.6 20.1 - - + +
134C ALA 3.5 17.0 + - - -
168C VAL* 1.3 71.1 - - - +
170C ILE* 1.3 67.7 + - - +
190C VAL* 3.0 37.5 + - + +
191C LEU* 4.1 9.1 - - - +
192C PHE* 4.7 8.8 - - - +
503C SAM 3.3 45.5 + - - +
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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