Contacts of the strand formed by residues 2386 - 2391 (chain B) in PDB entry 1V9P
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 PRO2386 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2349B ILE* 4.9 0.4 - - + -
2354B VAL* 4.2 35.4 - - + -
2356B ARG 4.5 9.4 - - - +
2357B VAL* 3.5 9.9 - - - +
2358B THR* 4.2 3.8 + - - +
2378B VAL* 4.5 2.9 - - + -
2379B HIS 2.9 12.8 - - - +
2380B LYS* 3.9 12.8 - - + -
2384B VAL 3.2 6.5 - - - +
2385B ILE* 1.3 91.4 - - + +
2387B GLU* 1.3 66.4 + - - +
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Residues in contact with GLU2387 (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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2196B VAL* 5.3 1.7 - - - +
2197B PHE 5.4 0.5 - - - +
2198B LYS* 5.0 12.5 - - - +
2357B VAL* 3.1 13.9 - - + -
2358B THR* 4.1 11.8 - - + +
2360B HIS* 2.7 37.2 + - - -
2364B TYR* 3.6 19.2 + - + -
2378B VAL* 3.4 7.2 - - - +
2379B HIS* 2.7 48.4 + - + -
2381B ALA* 4.5 15.2 - - + +
2385B ILE* 4.2 11.5 - - - +
2386B PRO* 1.3 77.4 - - - +
2388B VAL* 1.3 68.4 + - + +
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Residues in contact with VAL2388 (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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2198B LYS* 5.7 0.2 - - - +
2357B VAL* 3.7 9.4 - - + +
2358B THR 4.5 3.4 - - - +
2359B LEU* 3.6 30.7 - - + -
2364B TYR* 3.1 38.7 + - + -
2368B LEU* 5.5 2.0 - - + -
2370B ILE* 4.2 10.1 - - + -
2376B VAL* 3.8 26.5 - - + -
2377B LEU 3.4 7.6 - - - +
2378B VAL* 3.8 5.7 - - + +
2379B HIS* 4.5 1.4 - - - -
2387B GLU* 1.3 80.5 - - + +
2389B LEU* 1.3 63.3 + - - +
2390B ARG* 3.4 28.0 - - - +
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Residues in contact with LEU2389 (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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2198B LYS* 2.6 49.1 + - + +
2320B GLU* 5.0 15.3 - - - +
2368B LEU* 3.3 2.0 - - - +
2377B LEU* 2.7 28.4 + - + +
2379B HIS* 3.4 39.5 - - + +
2388B VAL* 1.3 75.4 - - - +
2390B ARG* 1.3 74.1 + - + +
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Residues in contact with ARG2390 (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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2368B LEU* 3.4 18.6 - - + -
2370B ILE* 6.6 0.2 - - - -
2376B VAL* 3.4 4.3 - - - +
2377B LEU* 3.3 42.1 + - + +
2388B VAL* 3.4 6.8 - - - +
2389B LEU* 1.3 94.2 - - + +
2391B VAL* 1.3 69.2 + - - +
2392B LEU* 2.8 37.1 + - - +
2394B GLU* 3.9 10.3 + - - -
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Residues in contact with VAL2391 (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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2368B LEU 3.2 27.0 + - - +
2369B ASP 3.6 8.7 - - - +
2370B ILE* 5.2 4.3 - - + -
2374B ASP* 3.2 36.8 - - + +
2375B TRP 3.1 16.8 - - - +
2376B VAL* 3.4 11.7 - - + -
2390B ARG* 1.3 85.9 + - - +
2392B LEU* 1.3 55.8 + - - +
2393B LYS* 2.7 48.3 + - + +
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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