Contacts of the helix formed by residues 93 - 100 (chain A) in PDB entry 2BKE
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 SER 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A SER* 5.3 0.2 - - - -
91A THR* 3.1 9.1 + - - -
92A GLY* 1.3 78.3 - - - +
94A GLN* 1.3 60.6 + - - +
95A ALA* 3.6 2.6 - - - +
96A LEU* 2.7 28.2 + - - +
97A ASP* 2.7 30.3 + - - +
312A PHE* 3.8 5.6 - - - +
319A ILE* 3.8 7.8 - - - +
320A ARG 3.7 19.5 - - - -
321A ASP* 3.0 17.6 + - - -
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Residues in contact with GLN 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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92A GLY 4.1 1.6 + - - -
93A SER* 1.3 70.0 - - - +
95A ALA* 1.3 63.8 + - - +
97A ASP* 3.2 12.3 + - - +
98A GLY* 2.9 21.3 + - - -
321A ASP* 2.9 20.2 + - - +
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Residues in contact with ALA 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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93A SER* 3.6 2.7 - - - +
94A GLN* 1.3 77.7 - - - +
96A LEU* 1.3 57.4 + - - +
98A GLY* 3.4 2.1 + - - -
99A LEU* 3.2 20.3 + - - +
310A VAL* 3.6 35.4 - - + +
311A VAL 3.6 15.3 - - - +
321A ASP* 2.9 17.9 + - + +
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Residues in contact with LEU 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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91A THR* 3.5 32.1 - - + +
93A SER* 2.7 22.4 + - - +
95A ALA* 1.3 72.4 - - - +
97A ASP* 1.3 63.3 + - - +
98A GLY 3.2 0.4 - - - -
99A LEU* 3.3 14.8 + - + +
100A LEU* 3.0 35.1 + - + +
112A PHE* 5.2 7.2 - - + -
123A LEU* 4.0 24.7 - - + -
285A ILE* 5.5 0.4 - - + -
297A ALA* 3.6 30.5 - - + -
310A VAL* 4.2 6.3 - - + -
312A PHE* 4.4 23.1 - - + -
319A ILE* 4.8 1.6 - - + -
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Residues in contact with ASP 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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90A SER* 2.5 35.7 + - - -
91A THR* 2.7 38.6 + - - +
93A SER 2.7 12.2 + - - +
94A GLN* 3.5 13.9 - - - +
96A LEU* 1.3 75.3 - - - +
98A GLY* 1.3 58.0 + - - +
100A LEU* 3.0 8.4 + - - -
101A ALA 3.1 0.2 + - - -
102A GLY* 2.6 44.6 + - - +
103A GLY* 3.3 8.0 + - - +
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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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94A GLN 2.9 13.9 + - - -
95A ALA 3.7 4.3 - - - -
96A LEU 3.2 0.2 - - - -
97A ASP* 1.3 73.5 - - - +
99A LEU* 1.3 61.3 + - - +
101A ALA* 2.8 20.5 + - - +
102A GLY 4.4 2.5 - - - -
306A PRO* 5.7 2.9 - - - +
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Residues in contact with LEU 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 ALA 3.2 13.1 + - - +
96A LEU* 3.5 26.2 - - + +
98A GLY* 1.3 75.0 - - - +
100A LEU* 1.3 58.7 + - + +
101A ALA 3.2 4.0 + - - -
285A ILE* 4.8 12.1 - - + -
297A ALA* 3.5 26.9 - - + +
298A ARG 4.6 0.4 - - - -
299A VAL* 4.4 21.8 - - + +
305A LEU* 3.7 18.0 - - - +
306A PRO* 4.5 9.3 - - + +
308A GLY* 3.1 37.5 - - - +
309A GLU* 4.2 7.4 - - - -
310A VAL* 4.1 8.3 - - + -
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Residues in contact with LEU 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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88A LYS* 3.5 5.0 + - - -
91A THR* 3.7 27.6 - - + -
96A LEU* 3.0 22.1 + - + +
97A ASP 3.0 8.5 + - - +
99A LEU* 1.3 82.1 - - + +
101A ALA* 1.3 69.8 + - - +
103A GLY* 3.5 33.0 - - - +
104A ILE* 4.1 12.6 - - + +
110A THR* 4.8 8.7 - - + -
112A PHE* 4.7 4.9 - - + -
283A ILE* 5.1 2.7 - - + -
285A ILE* 3.4 33.0 - - + -
305A LEU* 3.9 17.0 - - + +
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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