Contacts of the strand formed by residues 84 - 90 (chain I) in PDB entry 2BX5
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 ALA 84 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37I GLN* 3.9 25.4 - - + +
38I GLN 4.1 7.2 - - - +
39I LYS* 3.8 18.4 - - + +
40I PRO* 4.7 2.5 - - - -
82I ASP 2.6 18.4 + - - +
83I PHE* 1.4 73.5 - - - +
85I THR* 1.3 64.6 + - - +
86I TYR* 3.8 3.3 - - + -
102I THR 3.2 3.5 - - - +
103I LYS* 5.0 0.2 - - - -
104I VAL* 2.9 40.4 + - - +
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Residues in contact with THR 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36I TYR 3.9 0.2 - - - +
38I GLN* 3.0 36.4 + - - -
40I PRO* 4.6 8.7 - - - +
84I ALA* 1.3 76.3 + - - +
86I TYR* 1.3 64.6 + - - +
87I TYR* 3.5 39.4 + - + +
101I GLY* 4.0 13.7 - - - -
102I THR 3.8 6.5 - - - +
103I LYS* 4.5 27.5 + - + +
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Residues in contact with TYR 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I GLN* 2.4 32.0 + - - +
21I ILE* 3.7 15.3 - - + -
35I TRP* 5.1 3.8 - - + -
36I TYR 3.7 2.9 - - - +
37I GLN* 2.9 42.9 + - + -
47I LEU* 3.8 19.1 - - + -
62I PHE* 4.4 11.1 - + - -
73I LEU* 3.3 31.6 - - + -
75I ILE* 4.3 12.3 - - + +
78I LEU* 4.7 0.4 - - + +
82I ASP* 3.2 28.8 + - - +
84I ALA 3.8 9.0 - - - -
85I THR* 1.3 71.2 - - - +
87I TYR* 1.3 51.8 + - - +
101I GLY* 2.8 13.6 - - - -
102I THR 3.2 7.3 + - - +
104I VAL* 3.6 34.1 - - + -
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Residues in contact with TYR 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I GLN* 3.9 1.3 - - - -
34I ASN 3.5 0.2 - - - +
35I TRP* 3.3 4.3 - - - -
36I TYR* 2.6 46.8 + - + +
38I GLN* 4.0 29.7 + - + -
44I PRO* 5.4 4.0 - - + -
85I THR* 3.5 40.4 + - + +
86I TYR* 1.3 71.0 - - - +
88I CYS* 1.3 59.0 + - - +
98I PHE* 4.0 28.5 - + + -
99I GLY 3.9 13.0 - - - -
100I GLN* 3.7 8.1 - - - -
101I GLY* 3.3 27.8 - - - -
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Residues in contact with CYS 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I MET* 4.4 5.4 - - + -
6I GLN* 3.7 18.1 + - - -
23I CYS* 2.1 49.4 - - - -
33I LEU* 3.1 18.8 - - + -
34I ASN 3.2 5.2 - - - -
35I TRP* 3.7 17.1 - - + -
87I TYR* 1.3 74.4 - - - +
89I GLN* 1.3 59.0 + - - +
98I PHE* 3.7 4.7 - - - -
99I GLY* 3.0 35.5 + - - -
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Residues in contact with GLN 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I MET* 5.1 3.9 - - - +
33I LEU* 3.2 10.1 - - - +
34I ASN* 2.4 62.1 + - - +
36I TYR* 3.4 36.5 + - + -
88I CYS* 1.3 69.6 - - - +
90I GLN* 1.3 68.7 + - - +
91I SER* 4.3 5.9 + - - -
96I ASN* 4.0 21.7 + - + +
97I THR 3.2 16.2 - - - +
98I PHE* 3.2 34.2 - - + +
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Residues in contact with GLN 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2I ILE* 3.2 31.6 - - - +
4I MET* 4.3 15.5 - - + -
29I ILE* 4.9 11.0 - - + -
32I TYR 3.9 2.5 - - - -
33I LEU* 4.8 0.2 - - - +
34I ASN* 3.6 0.2 - - - +
89I GLN* 1.3 82.9 - - - +
91I SER* 1.3 54.6 + - - +
92I TYR* 2.7 23.1 + - + +
93I SER 3.1 24.5 + - - +
95I PRO 2.9 26.3 + - - -
96I ASN* 2.7 20.0 - - - -
97I THR* 3.0 24.5 + - - +
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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