Contacts of the strand formed by residues 135 - 140 (chain D) in PDB entry 2BNQ
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 SER 135 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125D GLN* 3.3 29.8 + - - +
126D LEU 2.9 24.5 - - - -
127D ARG* 4.1 7.8 + - - -
133D ASP 5.5 0.2 + - - -
134D LYS* 1.3 80.2 - - - +
136D VAL* 1.3 68.2 + - - +
137D CYS* 5.8 0.9 - - - -
179D TRP* 4.1 9.5 - - - +
180D SER 5.2 3.8 + - - +
185D PHE* 5.7 2.9 - - - -
187D CYS* 5.6 0.9 - - - -
126E PHE* 3.6 6.4 - - - -
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Residues in contact with VAL 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D GLN* 3.5 5.4 - - - +
126D LEU* 2.9 44.1 + - + -
135D SER* 1.3 79.7 - - - +
137D CYS* 1.3 68.0 + - - +
138D LEU* 5.5 0.2 - - + -
177D VAL* 4.0 12.6 - - + -
178D ALA 3.6 8.5 - - - +
179D TRP* 3.9 6.1 - - + +
185D PHE* 5.7 0.2 - - - -
187D CYS* 4.4 0.2 - - - -
126E PHE* 3.6 15.0 - - + -
142E VAL* 3.4 32.3 - - + -
144E LEU* 3.4 35.4 - - + -
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Residues in contact with CYS 137 (chain D).
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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123D VAL* 4.6 1.8 - - + -
124D TYR 3.3 5.2 - - - +
135D SER* 5.8 1.3 - - - -
136D VAL* 1.3 74.0 - - - +
138D LEU* 1.3 61.5 + - - +
139D PHE 4.1 0.6 + - - -
176D ALA 3.9 0.3 - - - +
177D VAL* 3.5 5.9 - - - +
178D ALA* 2.8 39.4 + - - +
185D PHE* 3.6 23.1 - - - -
187D CYS* 2.0 60.6 - - + -
190D ALA* 4.1 11.4 - - + -
191D PHE* 4.2 7.5 - - + -
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Residues in contact with LEU 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D ALA 3.5 2.3 - - - +
123D VAL* 3.3 4.2 - - - -
124D TYR* 2.8 52.8 + - + +
126D LEU* 4.5 19.1 - - + -
136D VAL* 4.1 1.1 - - + -
137D CYS* 1.3 71.8 - - - +
139D PHE* 1.3 60.1 + - - +
140D THR* 3.8 21.2 + - + +
175D SER* 3.9 21.1 - - - +
176D ALA 3.7 12.8 - - - +
177D VAL* 4.0 16.4 - - + -
132E GLU* 4.6 3.8 - - - +
140E THR* 3.7 35.0 - - + +
142E VAL* 4.2 10.8 - - + -
191E ARG* 4.7 0.9 - - + -
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Residues in contact with PHE 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D PRO* 4.2 9.0 - - + -
122D ALA 3.3 15.0 - - - -
123D VAL* 3.7 11.7 - - + +
137D CYS 4.1 1.4 + - - -
138D LEU* 1.3 71.8 - - - +
140D THR* 1.3 58.7 + - - +
142D PHE* 3.4 39.4 - + - -
146D THR* 4.0 11.0 - - - -
147D ASN 5.8 0.9 - - - -
148D VAL* 4.5 10.5 - - + -
175D SER* 3.1 4.0 - - - -
176D ALA* 2.9 33.5 + - + +
191D PHE* 3.5 34.0 - + + -
194D SER* 6.0 0.9 - - - -
196D ILE* 3.6 49.8 - - + -
197D PRO* 4.0 9.4 - - + -
200D THR* 4.1 9.6 - - + -
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Residues in contact with THR 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D PRO* 3.4 0.7 - - - +
122D ALA* 2.9 30.3 + - + +
124D TYR* 3.5 36.3 - - + -
138D LEU* 4.1 14.7 - - + +
139D PHE* 1.3 77.2 - - - +
141D ASP* 1.3 93.3 + - - +
142D PHE* 3.3 6.9 + - - -
164D LEU* 6.1 0.5 - - - +
173D SER* 4.7 1.0 + - - -
174D ASN 3.0 12.9 + - - -
175D SER* 3.7 10.4 - - - -
132E GLU* 5.3 0.4 - - - +
140E THR* 5.3 0.5 + - - -
193E ARG* 4.1 11.1 + - - +
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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