Contacts of the helix formed by residues 96 - 105 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H ASP* 5.2 1.8 - - - +
60H GLY 5.1 0.8 + - - -
62H GLU* 3.9 22.8 + - - +
65H ASP* 2.7 38.6 + - - -
68H ARG* 4.1 3.2 - - - +
92H ASN* 2.8 22.6 + - - +
94H ARG 3.4 0.2 - - - -
95H ALA* 1.3 79.0 - - - +
97H TRP* 1.3 94.0 + - + +
99H PRO* 3.2 7.2 - - - +
100H GLU* 2.9 44.5 + - + +
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Residues in contact with TRP 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H VAL* 4.0 16.4 - - + -
10H GLY* 3.2 40.2 - - - -
11H ASP* 2.9 34.2 + - - +
59H ALA 4.4 1.1 - - - -
60H GLY 4.4 8.3 - - - -
68H ARG* 3.7 50.0 - - - -
72H TYR* 5.0 0.7 - - - -
80H ILE* 3.7 26.7 - - + -
81H CYS 5.0 0.7 - - - -
89H SER 4.9 1.1 - - - -
92H ASN* 3.0 33.5 + - + +
93H VAL* 3.8 8.1 - - + +
96H LYS* 1.3 95.2 - - + +
98H TYR* 1.3 66.9 + - - +
100H GLU* 3.9 9.1 - - + +
101H VAL* 3.0 30.5 + - + +
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Residues in contact with TYR 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80H ILE* 4.1 12.4 - - + +
93H VAL 2.9 20.4 + - - +
94H ARG* 4.7 4.9 - - + -
97H TRP* 1.3 75.6 - - - +
99H PRO* 1.3 71.1 - - + +
101H VAL* 4.0 1.4 - - - +
102H ARG* 3.0 61.2 + - + +
110H ILE* 4.6 5.2 - - + -
148H GLU 4.8 5.2 + - - -
149H ILE* 3.4 58.2 - - + -
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Residues in contact with PRO 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94H ARG 3.3 26.2 - - - +
95H ALA 3.8 10.5 - - - +
96H LYS 3.2 14.4 - - - +
98H TYR* 1.3 102.1 - - + +
100H GLU* 1.3 61.3 + - - +
102H ARG* 3.9 3.7 - - + +
103H HIS* 3.0 25.8 + - - +
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Residues in contact with GLU 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65H ASP* 4.4 5.2 - - - +
68H ARG* 3.1 34.2 + - - +
69H PRO* 4.7 7.9 - - + -
72H TYR* 2.6 34.3 + - + +
96H LYS* 2.9 32.5 + - + +
97H TRP* 3.9 9.6 - - + +
98H TYR 3.3 0.2 - - - -
99H PRO* 1.3 78.8 - - - +
101H VAL* 1.3 64.2 + - - +
103H HIS* 3.4 6.4 + - - +
104H HIS* 3.1 33.2 + - + +
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Residues in contact with VAL 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H VAL* 4.0 25.4 - - + -
72H TYR* 4.5 14.6 - - + +
78H PHE* 3.4 48.7 - - + -
80H ILE* 4.2 9.9 - - + -
97H TRP* 3.0 20.1 + - + +
98H TYR 4.1 2.2 - - - +
100H GLU* 1.3 75.9 - - + +
102H ARG* 1.3 58.2 + - - +
104H HIS* 3.2 4.0 + - - +
105H CYS* 2.7 32.9 + - - +
110H ILE* 4.4 14.6 - - + -
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Residues in contact with ARG 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98H TYR* 3.0 50.1 + - + +
99H PRO* 4.2 3.6 - - + +
101H VAL* 1.3 77.4 - - - +
103H HIS* 1.3 63.8 + - - +
105H CYS 2.9 18.5 + - - -
106H PRO* 3.1 49.4 + - + +
107H HIS* 4.0 7.4 + - - +
108H THR* 2.8 36.3 + - - +
109H PRO* 4.9 0.6 - - - +
110H ILE* 3.4 33.1 - - + +
149H ILE 4.7 2.0 + - - -
150H GLY 4.3 13.3 + - - -
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Residues in contact with HIS 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F GLU* 5.6 3.4 + - - -
99H PRO 3.0 19.1 + - - +
100H GLU* 3.6 7.6 - - - +
101H VAL 3.2 0.2 - - - -
102H ARG* 1.3 79.0 - - - +
104H HIS* 1.3 83.2 + + + +
106H PRO* 5.0 3.6 - - - +
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Residues in contact with HIS 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69H PRO* 3.5 38.2 - - + +
72H TYR* 3.6 31.7 - + + -
100H GLU* 3.1 26.8 + - + -
101H VAL 3.2 3.6 + - - +
103H HIS* 1.3 102.0 - + + +
105H CYS* 1.3 61.1 + - - +
106H PRO* 3.8 7.1 - - - +
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Residues in contact with CYS 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72H TYR* 3.6 27.1 - - - -
73H PRO* 5.4 1.1 - - - -
74H GLN 5.7 0.7 - - - -
75H THR* 4.8 2.0 - - - -
78H PHE* 3.6 33.4 - - + -
101H VAL 2.7 15.6 + - - +
102H ARG* 2.9 22.7 + - - -
104H HIS* 1.3 80.9 - - - +
106H PRO* 1.3 69.3 - - - +
107H HIS 3.1 2.6 + - - -
108H THR* 3.4 21.1 - - - +
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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