Contacts of the strand formed by residues 136 - 140 (chain A) in PDB entry 2B9E
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 ARG 136 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A LEU 4.4 4.8 + - - -
135A PRO* 1.3 75.5 - - - +
137A PHE* 1.3 62.8 + - - +
138A VAL* 4.0 7.6 + - + -
189A LEU 3.8 0.5 - - - +
190A VAL* 3.4 4.4 - - - -
191A PHE* 2.9 50.1 + - + +
192A PRO 3.7 6.3 - - - +
193A ALA 3.0 26.0 + - - +
194A GLN* 4.6 10.5 + - - +
195A THR 3.4 30.8 + - - +
196A ASP* 4.9 8.5 - - - +
197A LEU* 6.1 1.8 - - + -
198A HIS* 5.7 6.5 + - - -
210A LEU* 6.4 0.2 - - - +
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Residues in contact with PHE 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LEU* 5.1 1.8 - - + -
135A PRO* 3.4 30.7 - - + -
136A ARG* 1.3 72.6 - - - +
138A VAL* 1.3 67.1 + - - +
171A LEU* 3.8 14.1 - - + -
182A ASP* 3.5 20.6 - - - -
188A LEU* 3.6 23.8 - - + -
189A LEU 3.5 1.8 - - - -
190A VAL* 3.6 25.6 - - + -
210A LEU* 3.8 4.0 - - - +
211A GLN 3.4 37.6 + - - +
212A ASP* 4.7 3.6 - - - -
213A ARG* 3.6 31.4 - - + +
413A LEU* 3.4 22.9 - - + -
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Residues in contact with VAL 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ARG* 4.3 8.1 - - + +
137A PHE* 1.3 82.1 - - - +
139A ARG* 1.3 62.6 + - - +
140A VAL 3.6 0.7 + - - -
188A LEU* 3.6 2.9 - - - +
189A LEU* 2.8 58.6 + - + +
191A PHE* 3.6 20.9 - - + -
197A LEU* 3.6 20.9 - - + -
208A LEU* 4.7 15.7 - - + -
209A ILE 3.6 4.9 - - - +
210A LEU* 3.5 25.4 - - + -
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Residues in contact with ARG 139 (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 VAL* 1.3 72.1 - - - +
140A VAL* 1.3 72.0 + - - +
141A ASN* 3.4 10.4 + - - +
186A PRO 5.4 2.7 - - - -
187A GLU* 3.5 17.3 - - + +
188A LEU* 3.7 13.6 - - + +
208A LEU* 3.5 4.1 - - - -
209A ILE* 2.8 65.9 + - - +
211A GLN* 2.9 33.2 + - + +
216A CYS* 4.4 6.1 - - - -
239A ASN 3.5 0.4 + - - -
242A SER* 2.8 31.7 + - - -
243A HIS* 3.4 50.7 - - - +
246A ALA* 4.3 11.1 - - - +
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Residues in contact with VAL 140 (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 VAL 4.7 0.7 - - - +
139A ARG* 1.3 80.0 + - - +
141A ASN* 1.3 63.2 + - - +
142A THR* 3.2 15.4 + - + +
145A THR* 3.9 13.7 - - + -
146A CYS* 3.7 11.0 - - - +
147A SER* 3.7 40.2 - - - +
150A VAL* 4.0 9.6 - - + -
187A GLU* 2.8 29.7 + - + +
189A LEU* 3.7 31.4 - - + -
207A HIS 3.7 5.2 - - - -
208A LEU* 5.1 2.7 - - + +
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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