Contacts of the strand formed by residues 2393 - 2398 (chain B) in PDB entry 2OVP
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 ARG2393 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2389B PHE* 3.5 2.6 - - - -
2390B CYS 2.9 35.6 + - - +
2391B GLY 2.6 12.5 + - - +
2392B ASN* 1.3 117.3 + - + +
2394B ILE* 1.3 60.7 + - - +
2405B VAL* 3.9 18.4 - - + -
2406B TRP 3.1 5.4 - - - -
2407B SER* 3.4 19.2 + - - +
2409B VAL* 4.7 0.8 - - - +
2414B LEU* 2.9 34.5 - - - +
2429B MET* 3.6 13.9 - - - +
2432B ASN 6.1 1.8 - - - +
2448B ALA* 5.4 7.2 - - + -
2449B GLU* 4.9 11.7 + - - +
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Residues in contact with ILE2394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2376B LEU* 4.1 7.6 - - + -
2387B LEU* 3.6 17.0 - - + -
2388B GLN 3.2 6.3 - - - +
2389B PHE* 3.6 11.7 - - + -
2393B ARG* 1.3 74.1 - - - +
2395B VAL* 1.3 64.4 + - - +
2405B VAL* 3.1 2.4 - - - -
2406B TRP* 2.4 54.4 + - + -
2407B SER 4.6 0.2 - - - -
2408B ALA* 3.5 21.5 - - + +
2683B VAL* 3.2 49.4 - - + -
2697B LEU* 4.4 2.7 - - + -
2699B VAL* 3.4 25.1 - - + -
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Residues in contact with VAL2395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2386B CYS 3.6 0.5 - - - +
2387B LEU* 3.5 5.1 - - - -
2388B GLN* 2.7 42.0 + - + +
2394B ILE* 1.3 75.7 - - - +
2396B SER* 1.3 61.1 + - - +
2397B GLY 3.6 0.9 + - - -
2403B LEU* 3.9 17.5 - - + -
2404B LYS 3.2 7.0 - - - +
2405B VAL* 3.9 8.7 - - + -
2427B SER* 3.9 10.2 + - - +
2429B MET* 3.1 31.9 - - - -
2434B ILE* 3.2 43.1 - - + -
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Residues in contact with SER2396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2379B HIS* 2.7 29.3 + - - -
2384B ILE* 3.8 11.7 - - - -
2386B CYS 3.6 4.5 - - - -
2387B LEU* 4.0 3.3 - - - +
2394B ILE 4.0 1.0 - - - -
2395B VAL* 1.3 71.1 - - - +
2397B GLY* 1.3 60.5 + - - +
2403B LEU* 2.9 5.3 - - - -
2404B LYS 2.7 33.6 + - - -
2406B TRP* 2.6 25.8 + - - +
2697B LEU* 3.5 26.2 - - - -
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Residues in contact with GLY2397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2384B ILE* 2.9 8.7 - - - -
2385B THR* 2.6 33.5 + - - -
2386B CYS* 2.6 33.8 + - - -
2395B VAL 3.6 1.4 + - - -
2396B SER* 1.3 73.2 - - - +
2398B SER* 1.3 54.3 + - - -
2402B THR 3.8 4.3 - - - -
2403B LEU* 4.1 12.5 - - - +
2424B VAL* 4.1 1.1 - - - -
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Residues in contact with SER2398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2379B HIS* 2.9 25.7 - - - -
2382B HIS* 3.3 21.3 - - - +
2383B VAL 2.7 19.8 + - - -
2385B THR 3.9 0.4 - - - +
2397B GLY* 1.3 75.2 - - - -
2399B ASP* 1.3 54.1 + - - +
2400B ASP* 2.8 26.2 + - - -
2401B ASN 3.2 4.2 + - - -
2402B THR 2.9 8.1 + - - +
2424B VAL* 2.7 34.8 + - - +
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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