Contacts of the strand formed by residues 123 - 130 (chain B) in PDB entry 4WB7
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 HIS 123 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ILE* 4.9 4.6 - - + +
114B LEU* 3.9 28.0 - - + -
115B VAL 3.2 14.6 - - - +
116B LYS* 3.8 27.5 - - + +
121B GLY 3.7 14.9 + - - -
122B ASN* 1.3 75.9 - - - +
124B TYR* 1.3 72.0 + - - +
177B TYR* 4.0 18.4 + - + +
376B PRO* 4.3 19.5 + - + +
377B GLY* 4.1 25.2 - - - -
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Residues in contact with TYR 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PHE* 4.2 15.7 - + - -
114B LEU* 3.5 8.3 - - - +
115B VAL* 2.9 35.1 + - + +
117B HIS* 4.0 14.2 - + + -
120B THR* 4.9 0.5 + - - -
122B ASN* 3.6 45.9 + - + -
123B HIS* 1.3 79.1 - - - +
125B ALA* 1.3 60.9 + - - +
162B GLU* 4.0 30.9 - - + -
163B PHE* 3.9 24.2 - + - -
174B VAL* 3.5 21.1 - - + -
175B MET 3.3 15.7 - - - +
176B GLU* 4.5 3.8 - - - -
177B TYR* 3.7 9.4 - - - +
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Residues in contact with ALA 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LEU* 4.1 6.3 - - + -
112B VAL* 3.9 12.8 - - + -
113B MET 3.4 5.4 - - - -
124B TYR* 1.3 71.7 - - - +
126B MET* 1.3 62.3 + - - +
173B MET 3.6 1.9 - - - +
174B VAL* 4.5 0.9 - - - -
175B MET* 2.8 38.4 + - - +
176B GLU 4.1 0.7 - - - +
177B TYR* 3.9 6.7 - - - +
501B ATP 3.4 44.4 - - + +
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Residues in contact with MET 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 3.9 21.3 - - + -
98B PHE* 4.8 9.6 - - + -
100B ARG* 4.0 16.4 - - + -
111B ARG 3.5 1.6 - - - +
112B VAL* 3.3 2.8 - - - -
113B MET* 2.8 37.0 + - + +
115B VAL* 3.8 29.6 - - + -
124B TYR 4.0 0.6 - - - -
125B ALA* 1.3 72.6 - - - +
127B LYS* 1.3 68.7 + - - +
128B ILE* 3.7 32.9 + - + +
165B PHE* 4.2 14.8 - - - -
172B TYR* 3.9 15.3 - - + -
173B MET 3.6 2.9 - - - +
174B VAL* 3.9 18.6 - - + +
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Residues in contact with LYS 127 (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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109B PHE* 5.6 0.4 - - - +
110B GLY* 4.5 3.1 - - - -
111B ARG 3.5 4.3 - - - +
112B VAL* 3.9 12.1 - - + -
125B ALA 3.7 1.6 + - - -
126B MET* 1.3 71.8 - - - +
128B ILE* 1.3 62.7 + - - +
129B LEU* 4.2 29.0 + - + +
146B GLU* 2.8 34.6 + - - +
171B LEU 3.7 0.9 - - - +
172B TYR* 3.3 7.6 - - - +
173B MET* 2.8 51.1 + - + +
175B MET* 3.9 18.2 - - + -
239B ASP* 3.5 4.9 + - - +
501B ATP 2.8 55.7 + - - +
503B ZN 4.2 0.2 - - - -
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Residues in contact with ILE 128 (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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110B GLY* 3.4 4.6 - - - -
111B ARG* 2.8 40.4 + - + +
113B MET* 4.0 23.1 - - + -
126B MET* 3.7 33.9 - - + +
127B LYS* 1.3 75.8 - - - +
129B LEU* 1.3 65.0 + - - +
130B ASP 4.3 0.9 + - - +
170B ASN* 4.0 21.5 - - + +
171B LEU 3.5 2.5 - - - -
172B TYR* 3.9 21.3 - - + -
390B ILE* 3.8 32.8 - - + -
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Residues in contact with LEU 129 (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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109B PHE* 3.5 41.3 - - + +
110B GLY* 3.6 7.6 - - - +
127B LYS* 4.2 12.8 - - + +
128B ILE* 1.3 75.2 - - - +
130B ASP* 1.3 61.1 + - - +
131B LYS 3.5 0.3 + - - -
134B VAL* 4.0 17.3 - - + -
143B THR* 3.6 26.5 - - + +
146B GLU* 4.5 4.7 - - - +
170B ASN* 3.2 8.1 - - - -
171B LEU* 2.8 49.5 + - + +
173B MET* 3.6 30.5 - - + -
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Residues in contact with ASP 130 (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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109B PHE 5.0 3.6 + - - -
128B ILE* 4.2 1.4 + - - +
129B LEU* 1.3 69.0 - - - +
131B LYS* 1.3 65.8 + - - +
132B GLN* 3.0 26.7 + - - +
133B LYS* 3.1 24.5 + - + +
134B VAL* 2.9 24.1 + - - +
169B SER* 4.3 5.1 - - - +
170B ASN* 3.4 16.8 + - - +
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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
------------------------------------------------------------
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