Contacts of the helix formed by residues 92 - 101 (chain A) in PDB entry 2BEW
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 GLU 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A ASN* 3.0 12.0 + - - +
90A TYR 4.0 6.4 - - - +
91A GLY* 1.3 80.2 - - - +
93A GLU* 1.3 63.9 + - - +
94A GLY 3.2 2.9 - - - -
95A THR* 2.7 32.4 + - - +
96A HIS* 3.2 16.1 - - - +
114A ARG* 3.4 17.8 - - - +
220A ARG* 2.8 40.4 + - - +
222A ASN* 2.9 30.5 + - - +
285A THR* 3.8 19.9 - - + +
286A TYR 4.2 3.8 - - - +
287A ARG* 3.6 9.5 - - - +
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Residues in contact with GLU 93 (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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64A MET* 3.8 35.4 - - + +
67A LEU* 4.0 21.1 - - + -
68A ASN* 3.2 27.3 + - + +
71A ASP* 5.1 0.2 - - - +
89A ASN* 3.5 13.5 + - + +
90A TYR* 3.5 14.4 - - - -
91A GLY* 2.9 19.6 + - - -
92A GLU* 1.3 78.3 + - - +
94A GLY* 1.3 60.7 + - - +
96A HIS* 3.3 13.2 + - - +
97A VAL* 3.2 26.9 + - - +
314A HIS* 3.5 10.3 - - - -
315A PRO* 3.8 1.2 - - - +
316A ILE* 3.9 10.9 - - + +
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Residues in contact with GLY 94 (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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64A MET* 3.7 9.3 - - - +
92A GLU 3.2 0.8 - - - -
93A GLU* 1.3 77.6 - - - +
95A THR* 1.3 64.1 + - - +
97A VAL* 4.3 0.2 - - - -
98A GLY* 3.0 23.7 + - - -
255A GLY 4.0 7.2 - - - -
258A VAL* 3.6 26.6 - - - +
261A VAL* 4.2 5.0 - - - +
315A PRO* 3.8 14.5 - - - +
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Residues in contact with THR 95 (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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92A GLU* 2.7 24.1 + - - +
94A GLY* 1.3 77.6 - - - +
96A HIS* 1.3 61.4 + - - +
99A SER* 2.7 35.9 + - - -
190A TYR* 4.8 0.8 - - - -
218A PHE* 4.0 18.3 - - + -
220A ARG* 4.0 10.6 - - + -
255A GLY* 3.4 21.0 + - - +
261A VAL* 3.7 9.5 - - - +
283A ALA* 3.9 21.5 - - + -
285A THR* 4.3 19.1 - - + +
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Residues in contact with HIS 96 (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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67A LEU* 3.9 5.4 - - + +
89A ASN* 3.2 40.4 - - + -
92A GLU* 3.2 24.3 + - - +
93A GLU* 3.3 5.4 + - - +
94A GLY 3.2 1.0 - - - -
95A THR* 1.3 90.0 + - - +
97A VAL* 1.3 59.6 + - + +
99A SER* 3.2 4.7 + - - -
100A ALA* 3.0 29.8 + - - +
114A ARG 2.7 23.3 + - - -
115A GLU* 3.6 15.7 - - + -
117A GLY* 3.0 35.0 + - - -
118A VAL* 3.7 13.3 - - + +
190A TYR* 5.3 2.7 - + - -
220A ARG* 4.4 4.2 - - - -
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Residues in contact with VAL 97 (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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60A LEU* 3.4 23.7 - - + +
63A SER* 3.9 23.1 - - - -
64A MET* 3.3 47.8 - - + +
67A LEU* 6.2 0.4 - - + -
93A GLU* 3.2 7.1 + - + +
96A HIS* 1.3 80.9 - - + +
98A GLY* 1.3 68.3 + - - +
100A ALA* 4.1 5.3 - - - +
101A ALA* 3.0 27.2 + - - +
117A GLY* 4.0 17.0 - - - +
121A TYR* 4.6 5.9 - - + -
258A VAL* 4.1 8.5 - - + -
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Residues in contact with GLY 98 (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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60A LEU* 4.5 5.4 - - - -
94A GLY 3.0 17.4 + - - -
97A VAL* 1.3 81.2 - - - +
99A SER* 1.3 61.9 + - - +
101A ALA 3.7 1.2 + - - -
102A ALA* 3.7 0.7 + - - +
258A VAL* 3.7 23.6 - - - -
261A VAL* 3.7 7.2 - - - -
262A TYR* 3.3 31.1 - - - -
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Residues in contact with SER 99 (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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95A THR 2.7 25.6 + - - -
96A HIS 3.2 2.8 + - - -
98A GLY* 1.3 77.0 - - - +
100A ALA* 1.3 65.0 + - - +
102A ALA 3.1 10.9 + - - -
103A LEU* 3.4 14.3 + - - +
188A ILE* 4.6 0.7 - - - -
190A TYR* 2.7 30.7 + - - -
218A PHE* 3.7 16.8 - - - -
261A VAL* 3.4 1.8 - - - +
265A THR* 3.6 30.8 - - - +
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Residues in contact with ALA 100 (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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96A HIS 3.0 20.1 + - - +
97A VAL 4.1 1.1 - - - +
99A SER* 1.3 77.7 + - - +
101A ALA* 1.3 62.9 + - - +
103A LEU* 3.1 30.7 + - + +
118A VAL* 4.0 30.3 - - + +
121A TYR* 4.0 26.1 - - + -
122A ARG* 5.4 6.2 + - + +
190A TYR* 4.5 0.7 - - - -
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Residues in contact with ALA 101 (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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56A LYS* 3.3 30.7 + - - -
60A LEU* 3.7 14.4 - - + -
97A VAL 3.0 19.2 + - - +
99A SER 3.2 0.4 - - - -
100A ALA* 1.3 77.5 - - - +
102A ALA* 1.3 58.0 + - - +
103A LEU 3.3 5.0 + - - +
121A TYR* 3.5 31.5 + - + +
262A TYR* 3.5 14.3 + - + -
266A LYS* 5.0 1.9 + - - -
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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