Contacts of the strand formed by residues 129 - 134 (chain A) 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 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A VAL* 3.5 28.2 - - - +
80A ILE 3.8 16.0 + - - +
81A PHE* 3.4 10.9 - - + +
82A ALA 3.1 21.1 + - - -
127A HIS* 3.7 2.7 + - - -
128A LYS* 1.3 84.1 - - + +
130A LEU* 1.3 67.8 + - - +
165A ARG* 3.6 40.6 - - + +
167A ASN* 4.7 7.3 - - - +
265A HIS* 5.8 2.2 + - - -
329A GLN* 3.8 29.7 + - - +
379A TYR* 4.3 7.4 - - - +
380A CYS 2.7 33.9 + - - -
381A THR* 3.6 20.0 - - + +
502A SF4 4.6 2.0 - - - -
505A ALA* 4.7 0.6 + - - -
506A H2S 3.9 19.4 - - - -
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Residues in contact with LEU 130 (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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81A PHE* 5.1 2.2 - - - -
82A ALA* 3.3 22.0 - - + +
84A LEU* 4.4 13.2 - - + -
119A VAL* 4.4 8.3 - - + -
122A LEU* 3.7 36.1 - - + -
127A HIS* 4.3 4.0 - - + -
129A ARG* 1.3 84.3 - - - +
131A ALA* 1.3 56.5 + - - +
132A VAL* 4.1 0.9 - - + +
153A ILE* 3.9 17.7 - - + -
163A ILE* 3.7 39.5 - - + -
165A ARG 3.2 6.9 + - - +
166A VAL* 3.4 7.6 - - + -
167A ASN* 2.8 34.2 + - - +
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Residues in contact with ALA 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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81A PHE* 4.3 19.9 - - + -
82A ALA 3.0 11.8 + - - +
83A PRO* 3.4 4.7 - - + +
84A LEU* 2.9 26.4 + - - -
130A LEU* 1.3 73.9 - - - +
132A VAL* 1.3 64.5 + - - +
133A GLU* 3.5 16.0 + - - +
167A ASN* 3.5 21.3 - - + +
169A ASN* 5.8 2.5 - - + +
190A VAL* 6.1 2.7 - - + -
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Residues in contact with VAL 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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84A LEU* 3.6 10.3 - - + -
86A VAL* 4.2 25.6 - - + -
130A LEU* 5.6 1.6 - - + -
131A ALA* 1.3 71.1 - - - +
133A GLU* 1.3 64.4 + - - +
134A ALA* 5.0 0.4 - - + +
146A ILE* 4.6 14.8 - - + -
149A VAL* 4.4 9.0 - - + -
150A ILE* 4.6 2.9 - - + -
153A ILE* 3.6 30.7 - - + -
166A VAL* 3.6 18.6 - - + -
167A ASN 2.8 13.2 + - - +
168A VAL* 4.3 14.0 - - + +
169A ASN* 2.8 29.8 + - - +
170A ILE* 5.3 0.7 - - + -
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Residues in contact with GLU 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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83A PRO* 4.4 8.5 - - + +
84A LEU 2.9 8.4 + - - +
85A TYR* 3.5 35.3 - - + +
86A VAL* 3.1 27.5 + - - +
87A SER 4.0 0.7 + - - +
131A ALA* 3.8 20.2 - - - +
132A VAL* 1.3 76.5 - - - +
134A ALA* 1.3 62.2 + - - +
169A ASN* 3.3 34.7 + - - +
192A PHE* 5.9 1.0 - - - -
354A GLN* 5.2 0.3 - - - +
503A MET* 3.1 29.7 - - + +
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Residues in contact with ALA 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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86A VAL* 4.3 5.6 - - + -
87A SER 3.4 8.1 - - - +
132A VAL* 5.3 0.2 - - + -
133A GLU* 1.3 75.6 - - - +
135A GLY* 1.3 70.8 + - - +
141A CYS* 3.9 10.5 - - - -
146A ILE* 3.9 27.8 - - + -
169A ASN 3.5 9.3 + - - +
170A ILE* 4.1 14.2 - - + +
171A ALA 4.7 0.7 + - - -
503A MET* 3.5 26.1 - - - +
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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