Contacts of the strand formed by residues 134 - 142 (chain A) in PDB entry 2BTO
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 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A ASN* 4.2 3.4 + - - -
5A ASN* 3.8 7.0 - - - +
7A ILE* 4.8 5.6 - - + -
128A ILE* 4.7 20.2 - - + +
131A CYS* 4.0 25.7 + - + +
132A ASP 4.2 0.2 - - - -
133A ASN* 1.3 74.7 + - - +
135A GLY* 1.3 62.0 + - - +
136A GLY 4.1 13.7 - - - +
137A ILE* 5.0 0.7 - - + -
166A ILE* 3.7 43.6 - - + +
167A PRO* 5.4 1.7 - - - +
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Residues in contact with GLY 135 (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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4A ASN* 3.5 26.0 - - - -
5A ASN 2.7 16.1 + - - -
6A THR* 5.1 0.9 - - - -
133A ASN 3.3 2.4 + - - -
134A VAL* 1.3 73.8 - - - +
136A GLY* 1.3 55.2 + - - +
167A PRO* 3.4 25.1 - - - +
255A SER* 5.0 4.0 - - - -
256A LEU* 3.9 14.3 - - - +
257A ARG* 4.0 7.0 + - - +
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Residues in contact with GLY 136 (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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5A ASN 3.3 3.5 + - - +
6A THR* 3.2 12.5 + - - +
7A ILE* 3.1 23.6 + - - +
134A VAL* 3.7 3.9 - - - +
135A GLY* 1.3 81.4 - - - +
137A ILE* 1.3 63.8 + - - -
166A ILE* 4.0 7.4 - - - -
167A PRO 3.5 11.9 - - - -
256A LEU* 4.2 12.0 - - - +
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Residues in contact with ILE 137 (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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7A ILE* 3.3 22.2 - - + +
9A VAL* 3.8 26.0 - - + -
124A LEU* 3.9 10.5 - - + -
128A ILE* 3.9 32.8 - - + -
134A VAL* 5.0 1.1 - - + -
136A GLY* 1.3 74.1 - - - -
138A ILE* 1.3 68.7 + - - +
139A VAL* 4.5 4.0 - - + -
159A LEU* 3.9 26.7 - - + -
166A ILE* 3.5 23.6 - - + -
167A PRO 3.1 6.6 + - - +
168A VAL* 3.5 10.7 - - + +
169A LEU* 3.1 23.6 + - - +
256A LEU* 4.5 1.0 - - - +
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Residues in contact with ILE 138 (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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6A THR* 3.9 22.9 - - + -
7A ILE 2.8 12.0 + - - +
8A VAL* 3.4 11.9 - - + +
9A VAL* 2.8 28.2 + - - +
22A PHE* 6.0 0.4 - - + -
52A PHE* 4.3 6.7 - - + -
137A ILE* 1.3 77.0 - - - +
139A VAL* 1.3 64.8 + - - +
140A LEU* 3.9 25.8 - - + -
169A LEU* 3.3 28.7 - - + +
171A CYS* 4.0 15.0 - - - -
237A LEU* 5.8 2.7 - - + -
240A ILE* 6.5 0.2 - - + -
241A THR* 4.2 24.9 - - + -
244A MET* 4.8 8.3 - - + -
256A LEU* 4.8 4.7 - - + -
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Residues in contact with VAL 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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9A VAL* 3.3 12.6 - - + +
11A ILE* 3.8 27.8 - - + -
137A ILE* 4.5 11.2 - - + -
138A ILE* 1.3 76.3 - - - +
140A LEU* 1.3 56.8 + - - +
141A HIS* 3.3 25.1 - - + +
152A GLY* 5.2 0.2 - - - -
155A LEU* 4.9 6.7 - - + -
156A ILE* 3.5 34.8 - - + -
159A LEU* 5.2 2.9 - - + -
168A VAL* 4.1 11.2 - - + -
169A LEU 2.8 12.0 + - - +
170A SER* 3.5 1.5 - - - -
171A CYS 2.8 30.2 + - - -
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Residues in contact with LEU 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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8A VAL* 4.1 18.2 - - + -
9A VAL 3.1 5.7 + - - +
10A SER* 3.4 3.4 - - - -
11A ILE* 2.9 27.5 + - - +
15A GLY* 3.7 13.0 - - - +
18A ILE* 4.0 16.2 - - + -
19A ALA* 3.8 39.3 - - + +
22A PHE* 5.0 4.5 - - + -
138A ILE* 3.9 15.0 + - + -
139A VAL* 1.3 69.5 - - - +
141A HIS* 1.3 61.6 + - - +
171A CYS* 3.6 26.7 - - + +
237A LEU* 3.8 20.6 - - + -
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Residues in contact with HIS 141 (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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11A ILE* 3.7 22.4 - - + +
15A GLY* 4.1 5.5 - - - -
18A ILE* 6.3 0.2 - - - +
139A VAL* 3.3 30.9 + - + +
140A LEU* 1.3 75.5 - - - +
142A ALA* 1.3 58.9 + - - +
143A ILE* 3.6 21.2 - - + +
148A GLY* 2.8 30.6 + - - +
149A SER* 5.6 0.2 - - - -
152A GLY* 4.3 11.0 - - - -
153A ALA* 5.4 0.4 - - - -
156A ILE* 5.3 1.3 - - + -
170A SER* 2.7 28.8 + - - -
171A CYS 3.2 12.6 + - - +
172A ALA* 3.4 3.4 - - - +
173A VAL* 3.0 25.4 + - - +
192A ALA* 5.8 1.1 - - + -
196A LEU* 4.0 13.7 - - + -
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Residues in contact with ALA 142 (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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11A ILE 4.4 2.0 + - - -
14A ALA* 3.5 25.5 - - + +
15A GLY 4.3 1.2 - - - +
141A HIS* 1.3 73.9 - - - +
143A ILE* 1.3 60.2 + - - +
144A GLY 3.5 0.7 - - - -
145A GLY 4.8 1.6 + - - -
148A GLY* 3.3 26.3 + - - -
149A SER 3.5 0.5 + - - -
173A VAL* 3.4 17.3 - - + +
1433A GTP 3.5 41.4 + - - +
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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