Contacts of the strand formed by residues 134 - 142 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B ASN* 3.6 11.7 - - - +
7B ILE* 4.8 7.6 - - + -
128B ILE* 4.4 24.0 - - + +
131B CYS* 4.2 17.9 - - + +
133B ASN* 1.3 79.7 + - - +
135B GLY* 1.3 61.0 + - - +
136B GLY 3.9 15.0 - - - +
137B ILE* 5.1 0.4 - - + -
166B ILE* 3.9 40.4 - - + +
167B PRO* 5.3 2.1 - - - +
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Residues in contact with GLY 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ASN* 4.0 25.8 - - - -
5B ASN 2.8 13.0 + - - -
6B THR* 5.3 2.2 - - - -
133B ASN* 3.4 3.2 + - - -
134B VAL* 1.3 72.9 - - - +
136B GLY* 1.3 57.9 + - - +
167B PRO* 3.4 24.1 - - - +
255B SER* 5.9 0.3 - - - -
256B LEU* 4.0 14.7 + - - +
257B ARG* 4.4 6.2 + - - +
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Residues in contact with GLY 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ASN 3.6 3.2 + - - +
6B THR* 3.5 12.2 + - - +
7B ILE 3.3 20.8 + - - -
134B VAL* 3.6 6.7 - - - +
135B GLY* 1.3 79.9 - - - +
137B ILE* 1.3 66.6 + - - +
166B ILE* 4.0 6.1 - - - -
167B PRO 3.3 12.8 - - - -
256B LEU* 3.8 13.0 - - - -
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Residues in contact with ILE 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ILE* 3.3 23.1 - - + +
9B VAL* 4.1 21.1 - - + -
124B LEU* 4.3 7.4 - - + -
128B ILE* 4.0 25.8 - - + -
134B VAL* 5.1 0.9 - - + -
136B GLY* 1.3 78.5 - - - +
138B ILE* 1.3 70.3 + - - +
139B VAL* 4.0 5.1 + - + -
159B LEU* 3.7 44.2 - - + -
163B TYR* 5.8 0.2 - - + -
166B ILE* 4.3 16.2 - - + -
167B PRO 3.0 10.3 + - - +
168B VAL* 3.4 5.1 - - + +
169B LEU 3.0 26.2 + - - +
256B LEU* 4.3 1.0 - - - +
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Residues in contact with ILE 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B THR* 4.0 19.7 - - + -
7B ILE 2.9 10.7 + - - +
8B VAL* 3.4 16.7 - - + +
9B VAL* 2.7 32.7 + - - +
22B PHE* 6.2 0.7 - - + -
52B PHE* 4.8 0.2 - - + -
137B ILE* 1.3 75.6 - - - +
139B VAL* 1.3 58.9 + - - +
140B LEU* 3.5 28.0 + - + -
169B LEU* 3.4 25.6 - - + +
171B CYS* 4.2 13.5 - - - -
237B LEU* 5.7 3.4 - - + -
240B ILE* 6.4 0.9 - - + -
241B THR* 4.2 24.9 - - + -
244B MET* 5.4 3.8 - - + -
256B LEU* 4.6 10.5 - - + -
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Residues in contact with VAL 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 3.2 14.8 - - + +
11B ILE* 4.2 16.4 - - + -
137B ILE* 4.2 15.7 - - + -
138B ILE* 1.3 75.8 - - - +
140B LEU* 1.3 59.5 + - - +
141B HIS* 3.5 26.4 - - + +
152B GLY* 5.1 2.5 - - - -
155B LEU* 4.9 6.7 - - + -
156B ILE* 4.1 31.2 - - + -
159B LEU* 4.9 4.9 - - + -
168B VAL* 4.5 8.7 - - + -
169B LEU 2.9 12.9 + - - +
170B SER* 4.5 1.1 - - - -
171B CYS 2.8 33.5 + - - +
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B VAL* 3.8 20.4 - - + -
9B VAL 2.8 12.5 + - - +
10B SER* 3.3 8.3 - - - -
11B ILE* 3.0 26.0 + - - +
15B GLY* 3.5 9.3 - - - +
18B ILE* 4.3 13.5 - - + -
19B ALA* 3.9 29.6 - - + +
22B PHE* 4.9 7.2 - - + -
138B ILE* 3.5 30.5 + - + -
139B VAL* 1.3 69.8 - - - +
141B HIS* 1.3 61.7 + - - +
171B CYS* 3.7 21.5 - - + -
237B LEU* 4.0 21.8 - - + -
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Residues in contact with HIS 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ILE* 3.7 19.5 - - + +
15B GLY* 4.0 6.8 - - - -
18B ILE* 6.0 1.0 - - - +
139B VAL* 3.5 18.4 + - + +
140B LEU* 1.3 75.7 - - - +
142B ALA* 1.3 56.5 + - - +
143B ILE* 3.9 18.5 - - + +
148B GLY* 3.0 27.9 + - - -
149B SER* 5.6 0.4 - - - -
152B GLY* 4.1 7.7 - - - -
156B ILE* 4.3 10.3 - - + -
170B SER* 2.9 25.8 + - - -
171B CYS 3.1 19.0 + - - +
172B ALA* 3.2 12.4 - - - +
173B VAL* 2.8 34.5 + - - +
192B ALA* 5.9 0.9 - - + -
196B LEU* 4.1 13.7 - - + -
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Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ILE 4.5 2.4 + - - -
14B ALA* 3.3 31.2 - - + +
15B GLY 4.4 1.0 - - - +
141B HIS* 1.3 75.0 - - - +
143B ILE* 1.3 61.0 + - - +
144B GLY 3.6 0.4 - - - -
145B GLY 4.8 2.1 + - - -
148B GLY* 3.5 24.8 - - - -
149B SER 3.6 0.5 + - - -
173B VAL* 3.5 16.4 - - + +
1433B GTP 3.5 33.6 + - - +
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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