Contacts of the strand formed by residues 166 - 174 (chain B) in PDB entry 4R2G
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 166 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B VAL* 3.9 22.2 + - + +
4B VAL* 4.4 7.5 - - - +
5B LEU* 3.6 39.5 + - + +
162B LEU* 3.3 6.5 - - - +
163B GLN 2.8 35.0 + - - +
164B ASN* 3.9 7.0 - - + +
165B GLN* 1.3 80.0 - - - +
167B LYS* 1.3 74.4 + - + +
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Residues in contact with LYS 167 (chain B).
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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5B LEU* 3.9 4.1 - - - +
160B THR* 4.2 16.2 - - + -
161B VAL 3.4 7.4 - - - +
162B LEU* 4.9 3.4 - - + +
166B LYS* 1.3 94.2 - - + +
168B VAL* 1.3 64.6 + - - +
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Residues in contact with VAL 168 (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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5B LEU* 4.1 27.8 - - + +
6B GLY* 4.8 2.0 - - - +
7B LYS* 3.8 38.8 - - + +
98B PHE* 4.1 12.8 - - + -
160B THR* 3.6 4.6 - - - +
161B VAL* 2.9 62.1 + - + +
167B LYS* 1.3 76.7 - - - +
169B GLU* 1.3 65.3 + - - +
170B PHE* 4.4 4.7 - - + -
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Residues in contact with GLU 169 (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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7B LYS* 2.2 43.0 + - - +
158B THR* 3.3 24.6 - - + +
159B CYS 3.8 4.9 - - - +
160B THR* 4.6 9.4 - - + +
168B VAL* 1.3 77.7 - - - +
170B PHE* 1.3 64.8 + - - +
171B LYS* 3.2 33.9 - - + +
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Residues in contact with PHE 170 (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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7B LYS* 4.0 32.5 - - + +
8B LYS* 4.9 2.2 - - + -
98B PHE* 3.1 38.1 - - + -
99B GLY* 3.9 3.1 - - - -
100B LEU* 3.6 41.5 - - + -
157B TRP 3.7 0.2 - - - +
158B THR* 3.6 3.8 - - - +
159B CYS* 2.9 46.2 + - + +
161B VAL* 3.6 33.0 - - + -
168B VAL* 4.4 6.5 - - + -
169B GLU* 1.3 78.1 - - - +
171B LYS* 1.3 66.3 + - - +
172B ILE* 4.2 0.7 - - + -
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Residues in contact with LYS 171 (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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156B THR* 4.3 17.7 - - + -
157B TRP 3.2 9.6 - - - +
158B THR* 4.2 13.7 - - - +
169B GLU* 3.2 27.8 - - - +
170B PHE* 1.3 76.6 - - - +
172B ILE* 1.3 60.1 - - - +
173B ASP* 5.7 0.8 - - - -
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Residues in contact with ILE 172 (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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100B LEU* 4.5 22.4 - - + +
101B THR* 5.0 0.9 - - - -
102B ALA* 3.6 38.6 - - + +
105B ASP* 5.6 4.5 - - - +
116B LEU* 4.9 14.1 - - + -
156B THR* 3.7 1.2 - - - -
157B TRP* 3.0 52.8 + - + +
159B CYS* 5.1 2.7 - - - -
170B PHE* 4.2 1.1 - - + +
171B LYS* 1.3 74.6 - - - +
173B ASP* 1.3 77.8 + - - +
174B ILE* 3.7 6.1 + - + -
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Residues in contact with ASP 173 (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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105B ASP* 4.1 10.4 - - - +
155B GLY 3.6 4.7 - - - +
156B THR* 2.9 23.9 + - - +
171B LYS 5.6 1.0 - - - +
172B ILE* 1.3 85.2 - - - +
174B ILE* 1.3 66.4 + - - +
175B VAL* 6.0 0.4 - - - -
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Residues in contact with ILE 174 (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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102B ALA* 5.0 14.6 - - + -
103B ASN 5.4 0.9 - - - +
105B ASP* 4.6 15.3 - - - +
106B THR 5.2 0.2 - - - +
107B HIS* 3.9 34.1 - - + +
114B LEU* 4.6 16.2 - - + -
153B ASP* 3.9 9.2 - - + +
154B SER* 3.4 4.6 - - - -
155B GLY* 2.9 40.4 + - - +
157B TRP* 3.3 37.5 - - + +
172B ILE* 3.7 5.6 + - + +
173B ASP* 1.3 80.1 - - - +
175B VAL* 1.3 75.0 + - + +
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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