Contacts of the helix formed by residues 86 - 96 (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 SER 86 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83H SER* 3.1 19.4 + - - +
84H LEU 3.5 0.2 - - - -
85H VAL* 1.3 77.9 - - - +
87H PRO* 1.3 65.2 - - - +
88H ALA* 3.1 8.4 + - - +
89H SER* 2.6 51.8 + - - -
90H PHE* 3.3 3.1 + - - +
137H ILE* 5.1 0.9 - - - -
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Residues in contact with PRO 87 (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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84H LEU 5.3 1.1 - - - +
85H VAL 3.7 7.9 - - - +
86H SER* 1.3 86.4 - - - +
88H ALA* 1.3 56.1 + - - +
90H PHE* 3.2 3.3 + - + +
91H GLU* 3.0 32.0 + - + +
129H LEU* 4.2 11.0 - - + -
134H LEU* 4.2 33.2 - - + -
135H ALA 3.3 25.8 - - - +
137H ILE* 4.0 21.7 - - + -
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Residues in contact with ALA 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H ASP* 4.2 3.4 - - - +
86H SER* 3.1 7.5 + - - +
87H PRO* 1.3 78.8 - - - +
89H SER* 1.3 62.4 + - - +
91H GLU* 3.4 7.7 + - - +
92H ASN* 3.0 31.3 + - - +
134H LEU* 6.2 0.2 - - - +
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Residues in contact with SER 89 (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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11H ASP* 3.3 21.4 + - - -
14H VAL* 3.9 24.7 - - - -
81H CYS 5.0 0.7 - - - +
82H PHE* 3.5 10.5 - - - +
83H SER 3.0 23.5 + - - -
86H SER* 2.6 34.8 + - - -
88H ALA* 1.3 73.4 - - - +
90H PHE* 1.3 66.2 + - - +
92H ASN* 3.4 3.1 + - - +
93H VAL* 3.3 15.1 + - - +
97H TRP* 4.9 1.7 - - - -
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Residues in contact with PHE 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82H PHE* 3.5 46.7 - + + -
86H SER 3.3 0.8 + - - +
87H PRO 3.2 10.7 + - - +
88H ALA 3.2 0.4 - - - -
89H SER* 1.3 78.4 + - - +
91H GLU* 1.3 69.6 + - + +
93H VAL* 2.9 23.1 + - + +
94H ARG* 5.6 2.0 - - - -
137H ILE* 3.4 35.7 - - + -
141H GLN* 3.2 36.6 - - + -
142H GLY* 4.1 2.2 - - - -
145H MET* 3.5 45.0 - - + +
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Residues in contact with GLU 91 (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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87H PRO* 3.0 15.6 + - + +
88H ALA* 3.7 10.5 - - - +
90H PHE* 1.3 80.0 - - + +
92H ASN* 1.3 58.2 + - - +
94H ARG* 3.1 31.3 + - - +
95H ALA* 3.0 26.7 + - + +
145H MET* 4.8 0.9 - - - -
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Residues in contact with ASN 92 (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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11H ASP* 2.8 40.9 + - - +
88H ALA* 3.0 19.7 + - - +
89H SER 3.8 3.4 - - - +
90H PHE 3.2 0.6 - - - -
91H GLU* 1.3 74.9 - - - +
93H VAL* 1.3 59.6 + - - +
95H ALA* 3.7 17.1 - - - +
96H LYS* 2.8 32.0 + - + +
97H TRP* 3.0 15.8 + - - +
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Residues in contact with VAL 93 (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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80H ILE* 4.0 19.1 - - + -
81H CYS 4.5 2.5 - - - +
82H PHE* 3.8 21.3 - - + -
89H SER 3.3 12.0 + - - +
90H PHE* 2.9 18.2 + - + +
92H ASN* 1.3 77.4 - - - +
94H ARG* 1.3 56.9 + - - +
97H TRP* 3.9 8.7 - - + -
98H TYR* 2.9 31.4 + - - +
112H LEU* 3.8 20.9 - - + -
145H MET* 3.7 25.4 - - + -
149H ILE* 4.0 15.3 - - + -
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Residues in contact with ARG 94 (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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90H PHE* 5.6 2.0 - - - -
91H GLU* 3.1 28.5 + - - +
93H VAL* 1.3 79.5 - - - +
95H ALA* 1.3 67.1 - - - +
98H TYR* 4.7 9.0 - - + -
99H PRO* 3.3 19.2 - - - +
145H MET* 3.3 40.4 - - + +
148H GLU* 3.0 39.1 + - - +
149H ILE* 5.0 2.7 - - + -
22N HIS* 6.0 4.7 - - - -
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Residues in contact with ALA 95 (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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91H GLU* 3.0 17.1 + - + +
92H ASN* 3.8 16.6 - - - +
94H ARG* 1.3 83.1 - - + +
96H LYS* 1.3 58.9 + - + +
99H PRO* 3.8 9.1 - - - +
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Residues in contact with LYS 96 (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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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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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