Contacts of the helix formed by residues 95 - 101 (chain A) in PDB entry 2X9D
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 ASP 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A LEU* 4.5 0.9 - - + -
21A GLY* 3.0 9.4 - - - -
22A ILE* 2.6 51.0 + - + +
23A ASP 4.4 0.3 + - - -
93A TYR 3.5 0.8 + - - -
94A ARG* 1.3 82.4 + - - +
96A GLY* 1.3 53.6 + - - +
97A ALA 3.4 2.9 - - - -
98A LYS* 3.2 18.5 + - + +
99A VAL* 2.8 33.9 + - - +
149A GLN* 4.1 20.7 + - - +
150A GLU* 4.7 6.4 - - - +
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Residues in contact with GLY 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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59A ILE* 4.5 14.6 - - - +
89A ALA 5.7 0.2 - - - -
90A LEU* 3.6 21.6 - - - +
93A TYR* 3.3 9.6 + - - -
94A ARG 3.1 5.3 - - - -
95A ASP* 1.3 75.6 - - - +
97A ALA* 1.3 59.4 + - - +
99A VAL* 3.5 10.6 - - - +
100A HIS* 2.9 28.8 + - - +
149A GLN* 3.6 2.0 + - - -
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Residues in contact with ALA 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 LEU* 3.7 15.5 + - + +
96A GLY* 1.3 75.0 - - - +
98A LYS* 1.3 52.7 + - - +
100A HIS* 3.2 2.3 + - - +
101A LEU* 2.8 34.0 + - - +
142A LEU* 3.7 13.7 - - + +
145A VAL* 3.9 15.9 - - + -
146A LEU* 3.3 32.5 - - + +
149A GLN* 3.3 16.4 + - - +
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Residues in contact with LYS 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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22A ILE* 3.2 40.1 - - + +
23A ASP* 5.2 6.3 + - - -
95A ASP* 3.2 22.6 + - - +
97A ALA* 1.3 77.5 - - - +
99A VAL* 1.3 63.4 + - - +
101A LEU* 3.9 21.5 - - + +
146A LEU* 3.8 19.5 - - + -
150A GLU* 2.8 33.4 + - - +
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Residues in contact with VAL 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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17A LEU* 3.7 31.4 - - + -
22A ILE* 4.0 15.3 - - + -
49A ARG* 4.9 4.2 + - - -
52A LEU* 3.7 21.5 - - + +
55A LEU* 4.0 12.1 - - + -
56A ALA* 3.6 37.0 - - - +
59A ILE* 4.1 7.0 - - + -
95A ASP 2.8 19.7 + - - +
96A GLY* 3.5 8.5 - - - +
98A LYS* 1.3 77.1 - - - +
100A HIS* 1.3 64.4 + - - +
101A LEU 3.6 4.9 + - - +
103A THR* 4.6 4.2 - - - +
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Residues in contact with HIS 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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56A ALA* 4.3 14.3 + - - +
59A ILE* 6.3 2.2 - - + -
60A LEU* 3.8 33.2 - - + +
86A PHE* 3.6 20.2 - + - -
90A LEU* 3.5 18.4 - - + -
96A GLY 2.9 17.2 + - - +
97A ALA 3.6 2.7 - - - +
99A VAL* 1.3 76.2 - - - +
101A LEU* 1.3 65.9 + - - +
102A GLY 3.3 1.6 + - - -
103A THR* 3.0 36.9 + - - +
104A ARG 6.3 1.8 - - - -
142A LEU* 4.8 13.9 - - + -
1209A ITC 3.0 27.5 + - - -
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Residues in contact with LEU 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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49A ARG* 5.0 6.8 + - - -
97A ALA 2.8 19.4 + - - +
98A LYS* 3.9 21.0 - - + +
99A VAL 3.5 6.6 - - - +
100A HIS* 1.3 75.0 - - - +
102A GLY* 1.3 66.1 + - - +
103A THR* 4.9 0.3 - - - +
142A LEU* 4.4 22.4 - - + +
146A LEU* 4.8 15.0 - - + -
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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