Contacts of the strand formed by residues 165 - 172 (chain A) in PDB entry 4WMB
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 LYS 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A ALA 5.4 7.0 + - - +
134A GLU 3.8 16.2 + - - +
135A VAL* 3.5 19.9 - - + -
136A LEU 3.0 21.9 + - - -
164A PHE* 1.3 81.6 - - - +
166A CYS* 1.3 62.7 + - - +
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Residues in contact with CYS 166 (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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125A LEU* 4.6 2.0 - - - -
135A VAL* 4.7 0.7 - - - -
136A LEU* 3.4 25.4 - - - +
138A LEU* 3.6 32.1 - - - -
158A LEU* 3.9 29.1 - - + +
160A PRO* 4.7 3.4 - - + -
164A PHE* 3.6 15.0 + - + +
165A LYS* 1.3 80.2 - - - +
167A LYS* 1.3 63.2 + - - +
168A VAL* 4.3 1.8 + - - +
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Residues in contact with LYS 167 (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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135A VAL* 4.2 9.7 - - + +
136A LEU 2.9 7.5 + - - +
137A ASN* 3.4 24.9 - - - +
138A LEU* 2.8 32.7 + - - +
166A CYS* 1.3 73.7 - - - +
168A VAL* 1.3 66.6 + - - +
169A ILE* 3.8 18.3 - - + +
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Residues in contact with VAL 168 (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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138A LEU* 3.5 12.8 - - + -
140A PHE* 4.0 8.5 - - + -
151A LYS* 6.0 0.2 - - + -
154A LEU* 3.6 23.3 - - + -
158A LEU* 3.8 28.5 - - + -
166A CYS* 4.3 2.4 + - - +
167A LYS* 1.3 83.6 - - - +
169A ILE* 1.3 67.2 + - - +
170A PHE* 3.5 33.0 - - + -
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Residues in contact with ILE 169 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A HIS* 5.4 0.2 - - + -
137A ASN* 3.8 31.2 - - + +
138A LEU 2.8 11.9 + - - +
139A HIS* 3.3 28.3 - - + +
140A PHE* 2.7 33.6 + - - +
167A LYS* 3.8 22.9 - - + +
168A VAL* 1.3 80.4 - - - +
170A PHE* 1.3 68.7 + - - +
171A HIS* 3.6 24.0 - - + +
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Residues in contact with PHE 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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140A PHE* 3.3 32.5 - - + -
142A SER* 4.2 7.4 - - - +
147A ARG* 3.8 52.0 - - + +
150A ALA* 3.6 24.0 - - + -
151A LYS* 3.9 27.6 - - + -
154A LEU* 4.2 4.3 - - + -
168A VAL* 3.5 27.4 - - + -
169A ILE* 1.3 81.6 - - - +
171A HIS* 1.3 67.2 + - - +
172A ASP 4.4 0.2 + - - -
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Residues in contact with HIS 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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101A LEU* 5.0 0.7 - - + -
139A HIS* 2.9 45.7 - + + -
140A PHE 2.8 13.6 + - - +
141A VAL* 3.4 7.1 - - + -
142A SER* 3.1 27.5 + - - +
169A ILE* 3.6 14.8 - - + +
170A PHE* 1.3 79.0 + - - +
172A ASP* 1.3 62.0 + - - +
176A LEU* 3.7 27.4 - - + +
214A MET* 3.7 29.7 - - + +
215A PRO* 5.4 6.5 - - + -
218A ILE* 6.3 0.2 - - + -
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Residues in contact with ASP 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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141A VAL* 4.8 0.2 - - - -
142A SER 3.7 7.5 - - - +
143A GLU* 4.7 0.4 - - - -
144A GLU* 4.4 20.2 - - - +
170A PHE 4.3 0.4 + - - -
171A HIS* 1.3 70.1 - - - +
173A VAL* 1.3 71.9 + - - +
174A ALA* 3.0 21.3 + - - +
175A VAL* 3.1 29.0 + - + +
176A LEU* 3.0 25.6 + - - +
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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