Contacts of the strand formed by residues 63 - 67 (chain A) in PDB entry 2BHT
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 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A GLY 4.9 1.8 - - - +
62A ASP* 1.3 76.3 - - - +
64A LEU* 1.3 70.1 + - - +
86A ARG* 3.4 45.5 - - - +
88A LYS* 3.3 42.2 - - + -
109A GLU* 4.5 2.0 - - - +
134A GLU 4.1 13.5 - - - +
135A GLY* 3.6 4.8 - - - -
136A LYS* 3.1 22.5 + - - +
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Residues in contact with LEU 64 (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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49A ILE* 4.7 16.8 - - + -
58A ILE* 3.9 35.9 - - + -
62A ASP* 5.1 2.5 - - + -
63A VAL* 1.3 82.9 - - - +
65A ILE* 1.3 62.9 + - - +
66A GLU* 6.0 1.3 - - + -
76A LEU* 6.0 2.2 - - + -
80A ALA* 6.1 0.4 - - + -
85A TYR* 4.7 17.3 - - + -
86A ARG 2.9 9.5 + - - +
87A MET* 3.4 27.7 - - + +
88A LYS* 2.8 30.5 + - - +
136A LYS* 3.5 26.2 - - + +
138A LEU* 4.6 16.8 - - + -
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Residues in contact with ILE 65 (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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63A VAL* 5.0 0.2 - - + -
64A LEU* 1.3 81.1 - - - +
66A GLU* 1.3 73.1 + - - +
88A LYS* 3.6 14.1 - - + +
90A LEU* 3.6 11.7 - - + -
126A ALA* 4.3 5.8 - - - +
129A MET* 3.3 37.9 - - + -
130A ALA* 3.9 17.7 - - + +
134A GLU 3.6 6.7 - - - +
135A GLY* 3.6 38.8 - - - +
136A LYS 2.7 12.2 + - - +
137A LEU* 3.1 39.0 - - + +
138A LEU* 3.6 2.5 + - - +
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Residues in contact with GLU 66 (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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48A MET* 4.1 3.8 - - - +
64A LEU* 6.0 0.9 - - + -
65A ILE* 1.3 79.6 - - - +
67A ALA* 1.3 56.9 + - - +
68A THR* 5.5 1.3 - - - -
72A THR* 6.1 0.2 - - - -
76A LEU* 3.3 37.2 - - + -
87A MET* 4.7 3.6 - - + -
88A LYS 3.2 5.1 + - - -
89A LEU* 3.1 15.4 - - + +
90A LEU* 2.6 35.2 + - - +
137A LEU* 4.4 2.8 - - - +
138A LEU* 2.8 19.3 - - + +
139A ASP* 2.7 30.4 + - - -
140A GLN* 2.8 39.9 + - - +
141A PHE* 5.0 0.7 - - - -
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Residues in contact with ALA 67 (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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66A GLU* 1.3 76.0 + - - +
68A THR* 1.3 55.0 + - - +
90A LEU* 3.1 12.3 - - + +
119A MET* 4.1 4.0 - - + -
122A ALA* 3.1 40.8 - - + +
123A ARG* 3.7 14.1 - - + +
126A ALA* 4.1 7.0 - - + +
137A LEU* 5.0 0.8 - - - +
140A GLN* 2.5 33.4 + - - -
141A PHE* 3.6 7.6 - - + -
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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