Contacts of the strand formed by residues 64 - 67 (chain C) in PDB entry 1OHV
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 ARG 64 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C TYR* 3.3 56.1 - - - +
14C ASP* 5.1 2.6 - - - +
15C GLY 2.8 31.9 + - - +
16C PRO* 3.2 9.8 + - - +
17C LEU* 2.9 59.6 + - + +
18C MET* 4.0 1.4 - - - +
56C TYR* 3.9 16.2 - - + -
57C LEU 3.6 3.1 - - - +
58C VAL* 3.9 13.7 - - + +
62C GLY 3.6 3.6 + - - +
63C ASN* 1.3 72.9 - - - +
65C MET* 1.3 61.2 + - - +
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Residues in contact with MET 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C MET* 3.8 17.7 - - + -
22C VAL* 4.2 9.9 - - + -
45C PHE* 3.5 37.5 - - + -
56C TYR* 3.2 7.9 - - - -
57C LEU* 2.9 49.4 + - + +
59C ASP* 4.1 20.0 - - + +
63C ASN* 4.2 5.8 - - + +
64C ARG* 1.3 76.2 - - - +
66C LEU* 1.3 68.2 + - - +
67C ASP* 3.3 0.5 + - - -
430C ARG* 4.0 33.2 - - - +
433C GLY* 3.4 11.0 - - - +
434C VAL 4.6 0.2 - - - +
435C MET* 4.4 11.9 - - + +
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Residues in contact with LEU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C PRO* 4.3 4.0 - - + +
55C ASN* 3.9 26.0 - - + -
56C TYR* 3.6 23.1 - - + +
64C ARG 4.2 0.2 + - - -
65C MET* 1.3 68.7 - - - +
67C ASP* 1.3 59.2 + - - +
68C LEU* 3.5 27.3 + - + -
433C GLY 2.7 15.9 + - - +
434C VAL* 3.4 9.1 - - + +
435C MET 2.9 25.1 + - - -
456C HIS* 3.9 41.3 - - + +
459C LEU* 4.4 12.1 - - + -
460C PHE* 4.1 20.0 - - + +
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Residues in contact with ASP 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C ASN* 2.8 24.9 + - - +
57C LEU* 3.8 25.9 - - + +
65C MET 3.3 0.6 + - - +
66C LEU* 1.3 70.8 - - - +
68C LEU* 1.3 63.8 + - - +
69C TYR* 2.9 10.4 + - - +
70C SER* 2.9 27.9 + - - -
71C GLN* 4.3 2.1 + - - -
79C TYR* 2.4 35.6 + - + -
435C MET* 3.5 19.5 - - + +
448C PRO* 4.5 6.8 - - - +
449C THR* 4.7 7.6 + - + +
106D LEU* 5.3 0.5 - - - +
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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