Contacts of the helix formed by residues 96 - 105 (chain E) in PDB entry 2OV2
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 LYS 96 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11E ASP* 5.1 2.9 - - - +
60E GLY 5.0 0.8 + - - -
62E GLU* 3.4 26.5 + - - +
65E ASP* 2.8 33.7 + - - -
68E ARG* 4.1 2.6 - - - +
92E ASN* 2.9 21.4 + - - +
95E ALA* 1.3 79.3 - - + +
97E TRP* 1.3 97.7 + - + +
99E PRO* 3.3 7.2 - - - +
100E GLU* 2.8 45.9 + - + +
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Residues in contact with TRP 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E VAL* 4.1 16.2 - - + -
10E GLY* 3.2 41.1 - - - -
11E ASP* 2.8 34.9 + - - +
59E ALA 4.5 0.9 - - - -
60E GLY 4.2 7.2 - - - -
68E ARG* 3.5 52.5 - - - -
72E TYR* 5.0 1.1 - - - -
80E ILE* 3.9 25.6 - - + -
81E CYS 5.0 2.7 - - - -
89E SER 5.0 1.1 - - - -
92E ASN* 3.0 30.9 + - + +
93E VAL* 4.0 5.6 - - + +
96E LYS* 1.3 99.1 - - + +
98E TYR* 1.3 66.4 + - - +
100E GLU* 4.0 8.0 - - + +
101E VAL* 3.0 31.2 + - + +
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Residues in contact with TYR 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLY 6.1 0.2 - - - -
31A GLU* 2.6 49.0 + - + +
33A ILE* 5.1 2.8 - - - +
80E ILE* 4.0 12.7 - - + +
93E VAL 2.8 21.5 + - - +
94E ARG* 4.6 5.4 - - + -
97E TRP* 1.3 71.4 - - - +
99E PRO* 1.3 76.1 - - + +
101E VAL* 4.0 1.0 - - - +
102E ARG* 3.0 59.2 + - + +
110E ILE* 4.7 5.2 - - + -
148E GLU 4.8 2.5 - - - -
149E ILE* 3.4 56.9 - - + -
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Residues in contact with PRO 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E ARG 3.2 26.9 - - - +
95E ALA 3.7 14.1 - - - +
96E LYS* 3.3 11.4 - - - +
98E TYR* 1.3 102.2 - - + +
100E GLU* 1.3 61.3 + - - +
102E ARG* 4.0 3.2 - - + +
103E HIS* 3.1 25.3 + - - +
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Residues in contact with GLU 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E ASP* 4.3 5.5 - - - +
68E ARG* 3.0 35.0 + - - +
69E PRO* 4.3 7.0 - - - +
72E TYR* 2.6 34.9 + - + +
96E LYS* 2.8 37.1 + - + +
97E TRP* 4.0 10.1 - - + +
98E TYR 3.3 0.2 - - - -
99E PRO* 1.3 75.8 - - - +
101E VAL* 1.3 63.8 + - - +
103E HIS* 3.4 6.9 + - - +
104E HIS* 3.1 32.7 + - + +
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Residues in contact with VAL 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E VAL* 4.1 24.2 - - + -
72E TYR* 4.5 15.3 - - - +
78E PHE* 3.7 47.8 - - + -
80E ILE* 4.3 9.2 - - + -
97E TRP* 3.0 18.0 + - + +
98E TYR 4.1 1.6 - - - +
100E GLU* 1.3 75.1 - - + +
102E ARG* 1.3 58.3 + - - +
104E HIS* 3.1 5.7 + - - +
105E CYS* 2.8 32.3 + - - +
110E ILE* 4.3 16.6 - - + -
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Residues in contact with ARG 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ALA* 6.1 0.2 - - - +
98E TYR* 3.0 50.2 + - + +
99E PRO* 4.2 3.8 - - + +
101E VAL* 1.3 79.4 - - - +
103E HIS* 1.3 64.4 + - - +
104E HIS 3.2 0.6 + - - -
105E CYS 2.7 29.0 + - - -
106E PRO* 3.0 49.5 + - + +
107E HIS* 3.6 7.8 + - - +
108E THR* 3.0 33.7 + - - +
109E PRO* 5.0 0.4 - - - +
110E ILE* 3.2 33.6 - - + +
149E ILE 4.7 2.8 + - - -
150E GLY 4.4 12.3 + - - -
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Residues in contact with HIS 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E PRO 3.1 17.9 + - - +
100E GLU* 3.6 7.4 - - - +
101E VAL 3.2 0.4 - - - -
102E ARG* 1.3 76.8 - - - +
104E HIS* 1.3 83.2 + + + +
106E PRO* 5.3 2.8 - - - +
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Residues in contact with HIS 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E PRO* 3.7 36.0 - - + +
72E TYR* 3.6 26.3 - + + -
73E PRO* 6.4 0.4 - - + -
100E GLU* 3.1 26.2 + - + -
101E VAL 3.1 5.7 + - - +
103E HIS* 1.3 103.5 - + - +
105E CYS* 1.3 67.5 + - - +
106E PRO* 3.8 7.9 - - - +
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Residues in contact with CYS 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E TYR* 3.6 26.2 - - - -
73E PRO* 5.3 1.6 - - - -
74E GLN 5.5 1.1 - - - -
75E THR* 4.9 2.0 - - - -
78E PHE* 3.8 27.1 - - + -
101E VAL* 2.8 16.8 + - + +
102E ARG* 2.7 34.6 + - - -
104E HIS* 1.3 88.6 - - - +
106E PRO* 1.3 55.6 - - - +
107E HIS 3.3 3.1 - - - -
108E THR* 3.3 22.2 - - - +
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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