Contacts of the strand formed by residues 149 - 153 (chain A) in PDB entry 6BW4
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 VAL 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A ALA* 4.5 1.3 - - + -
142A THR 3.3 14.8 - - - +
143A LYS* 3.9 14.8 - - + +
147A SER 4.2 6.1 - - - +
148A ASP* 1.3 76.5 - - - +
150A LEU* 1.3 68.4 + - - +
173A LEU* 2.8 48.7 + - + +
176A HIS* 4.3 0.7 - - + -
183A LEU* 4.1 20.6 - - + -
193A LEU* 4.1 17.5 - - + -
195A SER* 3.7 16.2 - - - +
205A TRP* 3.6 24.2 - - + -
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Residues in contact with LEU 150 (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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123A HIS* 4.1 6.5 - - + +
124A GLU* 4.7 5.6 - - - +
140A ILE 3.8 0.4 - - - +
141A ALA* 3.2 5.7 - - - +
142A THR* 2.8 40.1 + - - +
144A THR* 3.6 26.7 - - + -
148A ASP* 3.8 13.5 - - + -
149A VAL* 1.3 81.6 - - - +
151A VAL* 1.3 64.5 - - - +
152A PHE* 3.6 17.7 - - + -
167A CYS* 4.0 26.9 - - - -
169A PRO* 4.0 7.0 - - + -
171A LEU 3.6 1.1 - - - -
172A ARG* 3.4 39.3 - - + +
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Residues in contact with VAL 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ILE* 3.5 30.5 - - + -
140A ILE 3.4 4.9 - - - +
141A ALA* 4.6 9.0 - - + -
150A LEU* 1.3 79.4 - - - +
152A PHE* 1.3 62.3 + - - +
153A ASP 4.3 0.2 - - - -
169A PRO* 3.8 1.0 - - - +
170A ASP* 2.8 32.7 + - + +
171A LEU* 3.0 28.7 + - + +
173A LEU* 3.9 27.1 - - + -
185A TRP* 4.6 3.6 - - + -
207A ILE* 4.5 12.1 - - + -
212A LYS* 4.4 16.8 - - + -
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Residues in contact with PHE 152 (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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79A LEU* 3.9 27.6 - - + -
121A ILE* 3.7 31.2 - - + -
122A ASN 3.9 8.7 - - - -
123A HIS* 3.8 20.0 - + - -
138A CYS 3.4 2.1 - - - +
139A ILE* 3.4 2.6 - - - +
140A ILE* 2.7 42.4 + - + +
142A THR* 3.9 9.9 - - + -
150A LEU* 3.6 26.9 - - + -
151A VAL* 1.3 78.3 - - - +
153A ASP* 1.3 62.4 + - - +
154A TYR* 3.7 2.0 + - + +
157A HIS* 3.8 13.7 - + - +
167A CYS* 3.9 21.1 - - - -
168A ASN 4.3 3.1 - - - -
169A PRO* 3.7 24.5 - - + -
170A ASP* 3.4 1.8 - - - +
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Residues in contact with ASP 153 (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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136A ASN* 5.4 2.3 + - - -
138A CYS* 3.4 17.3 - - - +
139A ILE* 3.8 24.5 - - + +
152A PHE* 1.3 69.0 - - - +
154A TYR* 1.3 59.0 + - - +
155A THR* 2.8 23.8 + - - -
156A LYS* 3.0 56.0 + - - +
157A HIS* 3.2 12.8 - - - -
170A ASP* 2.9 10.7 + - + +
212A LYS* 5.2 2.6 - - + +
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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