Contacts of the strand formed by residues 156 - 161 (chain A) in PDB entry 1R6W
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 LEU 156 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A LEU* 3.8 36.8 - - + -
128A LYS* 3.7 21.1 - - + +
130A ALA* 4.4 7.4 - - + +
149A LEU* 3.8 28.3 - - + +
150A LEU* 3.9 3.5 - - + +
153A ILE* 3.0 27.2 + - + +
155A ASP* 1.3 79.4 + - - +
157A HIS* 1.3 81.3 + - - +
158A LEU* 3.9 27.6 - - + -
185A ARG* 3.0 27.8 + - - +
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Residues in contact with HIS 157 (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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127A GLU* 5.5 7.2 - - + -
128A LYS 2.9 12.8 + - - +
129A VAL* 3.2 34.9 - - + +
130A ALA 3.2 5.2 + - - +
155A ASP* 3.1 24.3 + - - +
156A LEU* 1.3 78.6 + - - +
158A LEU* 1.3 62.4 + - - +
184A ASP* 4.9 4.7 + - - -
185A ARG* 3.2 35.1 - - + +
187A ALA* 4.6 14.8 - - + +
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Residues in contact with LEU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 5.0 2.0 - - + -
130A ALA* 3.5 17.7 - - + +
132A VAL* 4.1 21.3 - - + -
146A VAL* 4.1 16.6 - - + -
149A LEU* 4.0 25.6 - - + -
150A LEU* 3.7 30.3 - - + -
156A LEU* 3.9 22.6 - - + -
157A HIS* 1.3 73.3 - - - +
159A ARG* 1.3 58.6 + - - +
160A LEU* 4.1 16.8 - - + -
185A ARG 2.9 10.7 + - - +
186A ILE* 3.4 10.1 - - + +
187A ALA 2.8 28.1 + - - -
188A PHE 3.8 0.9 + - - -
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Residues in contact with ARG 159 (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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107A ALA* 3.7 21.2 - - - +
129A VAL* 3.5 29.7 - - + +
130A ALA 2.9 10.5 + - - +
131A LYS* 3.2 18.7 - - + -
132A VAL 2.9 25.6 + - - -
158A LEU* 1.3 75.3 - - - +
160A LEU* 1.3 64.4 + - - +
187A ALA* 4.3 8.0 - - + +
188A PHE* 3.4 48.1 - - + -
258A THR* 5.6 0.4 - - - +
260A VAL* 3.8 14.8 - - - +
285A THR* 3.8 17.0 - - - +
286A ILE* 2.8 40.0 + - - +
287A PRO 4.2 2.8 - - - -
288A GLY* 4.3 2.6 - - - +
735A 164 5.4 1.0 + - - -
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Residues in contact with LEU 160 (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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131A LYS* 5.1 1.6 - - - -
132A VAL* 3.2 26.2 - - + +
134A VAL* 4.4 11.2 - - + -
146A VAL* 4.0 21.3 - - + -
158A LEU* 4.2 14.6 - - + -
159A ARG* 1.3 84.1 - - - +
161A ASP* 1.3 63.3 + - - +
162A ALA 4.3 0.2 - - - -
174A PHE* 3.8 30.3 - - + -
186A ILE* 3.9 30.3 - - + -
188A PHE* 3.0 7.2 + - - +
189A LEU* 3.5 19.2 - - + -
190A GLU* 2.8 28.5 + - - +
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Residues in contact with ASP 161 (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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131A LYS* 3.4 17.0 + - - -
132A VAL 3.2 8.2 + - - +
133A ARG* 3.5 11.3 - - + +
134A VAL* 2.9 26.0 + - - +
160A LEU* 1.3 78.1 - - - +
162A ALA* 1.3 58.5 + - - +
163A ASN* 2.9 37.9 + - - +
190A GLU* 2.8 18.7 - - + +
191A GLU* 4.9 1.0 - - - +
735A 164 2.8 13.2 + - - -
736A MG 2.1 32.0 - - - -
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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