Contacts of the strand formed by residues 83 - 89 (chain A) in PDB entry 1BHL
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 TYR 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A TRP* 3.7 20.2 - + - -
76A ALA 3.7 0.2 - - - +
77A VAL* 3.4 2.4 - - - -
78A HIS* 2.9 26.8 + - + -
81A SER* 3.2 18.6 + - - +
82A GLY* 1.3 77.0 - - - +
84A ILE* 1.3 60.9 + - - +
85A GLU* 2.5 48.7 + - + +
107A ARG* 4.6 0.3 - - - -
108A TRP* 3.5 20.1 - + - -
184A ASN* 3.4 32.3 - - + -
196A ALA* 3.6 8.5 - - - +
197A GLY* 4.3 7.4 - - - -
200A ILE* 3.4 36.3 - - + -
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Residues in contact with ILE 84 (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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75A VAL* 4.5 10.8 - - + -
76A ALA 3.0 12.8 - - - +
77A VAL* 4.0 10.5 - - + -
82A GLY 3.5 11.4 - - - +
83A TYR* 1.3 87.9 - - - +
85A GLU* 1.3 66.9 + - - +
86A ALA* 5.1 0.2 - - + -
154A MET* 3.6 18.8 - - + -
158A LEU* 4.5 10.8 - - + -
180A VAL* 3.7 37.3 - - + +
183A HIS* 3.1 35.7 - - + +
184A ASN* 3.0 33.3 + - - +
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Residues in contact with GLU 85 (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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75A VAL* 3.7 1.7 - - - +
76A ALA* 2.9 31.2 + - + +
83A TYR* 2.5 34.1 + - + +
84A ILE* 1.3 74.0 - - - +
86A ALA* 1.3 62.4 + - - +
100A PHE* 3.9 15.4 - - + -
104A LEU* 3.1 24.4 - - + +
107A ARG* 2.7 35.2 + - - -
108A TRP* 2.7 20.6 + - - -
180A VAL* 4.7 4.3 - - + -
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Residues in contact with ALA 86 (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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73A ILE* 4.2 6.3 - - + -
74A LEU 3.1 13.5 - - - +
75A VAL* 4.6 8.3 - - + -
85A GLU* 1.3 76.9 - - - +
87A GLU* 1.3 70.6 + - - +
100A PHE* 4.3 3.4 - - - -
158A LEU* 5.0 3.1 - - + -
176A VAL* 3.9 15.3 - - + -
177A GLN* 3.0 21.9 + - - +
180A VAL* 3.7 25.4 - - + +
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Residues in contact with GLU 87 (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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73A ILE* 3.4 3.5 - - - +
74A LEU* 2.7 40.3 + - + +
86A ALA* 1.3 81.5 - - - +
88A VAL* 1.3 71.7 + - - +
89A ILE* 3.7 10.9 + - + -
100A PHE* 3.8 26.6 - - + -
103A LYS* 3.7 25.7 + - - +
176A VAL* 5.4 0.4 - - - -
177A GLN* 4.2 10.1 + - - +
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Residues in contact with VAL 88 (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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71A LYS* 4.3 26.0 - - + -
72A VAL 3.3 8.5 - - - +
73A ILE* 4.1 10.5 - - + -
87A GLU* 1.3 80.6 + - - +
89A ILE* 1.3 69.8 + - - +
90A PRO* 4.8 0.2 - - - +
172A LEU* 4.5 4.3 - - + -
173A LYS* 3.9 44.1 + - + +
176A VAL* 3.7 32.1 - - + -
177A GLN* 5.0 3.1 - - - +
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Residues in contact with ILE 89 (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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65A CAS 4.7 3.1 - - + -
71A LYS* 4.6 2.4 - - - +
72A VAL* 2.8 48.9 + - + +
74A LEU* 3.9 22.7 - - + +
87A GLU* 4.6 20.4 - - + +
88A VAL* 1.3 84.1 - - - +
90A PRO* 1.3 77.5 - - + +
91A ALA 3.2 24.9 - - - +
92A GLU* 4.2 4.9 - - - -
93A THR 5.4 0.2 - - - +
96A GLU* 3.6 37.0 - - + +
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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