Contacts of the helix formed by residues 2361 - 2368 (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 ASN2361 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2190B GLU* 3.4 35.1 + - - +
2193B GLY 3.5 9.6 + - - +
2194B GLU 2.4 29.8 + - - +
2195B LYS* 4.7 2.3 - - - +
2196B VAL* 4.8 3.4 + - - +
2337B ARG* 4.0 7.4 - - - +
2340B PRO* 3.3 12.0 - - - +
2359B LEU 2.4 15.1 + - - -
2360B HIS* 1.2 83.6 - - + +
2362B GLU* 1.3 76.5 - - + +
2364B TYR* 2.5 29.8 + - - +
2365B ILE* 3.7 1.1 + - - -
2405B TRP* 4.9 1.3 - - - -
2422B VAL* 4.9 1.6 - - + -
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Residues in contact with GLU2362 (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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2193B GLY* 4.9 0.9 - - - +
2337B ARG* 5.8 0.8 + - - -
2338B VAL 4.9 0.9 - - - +
2361B ASN* 1.3 77.0 - - + +
2363B SER* 1.3 66.1 + - - +
2364B TYR 3.2 0.3 + - - -
2365B ILE* 3.4 6.6 + - - +
2366B GLU* 3.2 34.3 + - - +
2405B TRP* 2.9 45.5 + - - -
2418B LYS* 4.6 6.4 + - - +
2421B LYS* 2.7 26.2 - - + +
2422B VAL* 2.8 15.8 - - + +
2423B HIS* 2.6 49.2 + - - +
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Residues in contact with SER2363 (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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2193B GLY 2.5 28.0 + - - -
2194B GLU* 3.8 14.3 - - - -
2195B LYS* 4.5 3.4 - - - -
2361B ASN* 2.6 3.2 + - - -
2362B GLU* 1.3 75.5 - - - +
2364B TYR* 1.3 67.7 + - - +
2366B GLU* 3.0 14.4 + - - +
2367B GLU* 2.7 34.3 + - - +
2421B LYS* 5.0 7.3 - - - +
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Residues in contact with TYR2364 (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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2195B LYS* 3.2 39.2 - - + +
2196B VAL* 4.2 17.5 - - + -
2198B LYS* 3.7 20.0 + - + +
2358B THR 5.2 1.1 - - - -
2359B LEU* 3.9 28.7 - - + +
2360B HIS* 4.4 6.1 - + + -
2361B ASN* 2.5 28.1 + - - +
2363B SER* 1.3 69.9 - - - +
2365B ILE* 1.3 68.4 + - - +
2366B GLU 2.6 2.1 + - - -
2367B GLU* 2.7 14.6 + - - +
2368B LEU* 3.0 31.5 + - + +
2370B ILE* 4.5 5.2 - - + -
2387B GLU* 3.6 16.8 + - - -
2388B VAL* 3.1 42.2 + - + -
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Residues in contact with ILE2365 (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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2328B VAL* 5.3 0.2 - - + -
2340B PRO* 3.7 22.0 - - + -
2359B LEU* 3.5 44.4 - - + +
2361B ASN 4.8 0.9 - - - +
2362B GLU 3.4 8.4 + - - +
2364B TYR* 1.3 78.5 - - - +
2366B GLU* 1.3 58.7 + - + +
2369B ASP* 3.1 21.0 + - - -
2370B ILE* 3.1 41.0 + - + +
2403B ILE* 3.9 32.1 - - + +
2405B TRP* 3.9 11.0 - - + -
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Residues in contact with GLU2366 (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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2362B GLU* 3.2 27.5 + - - +
2363B SER* 3.0 11.4 + - - +
2364B TYR 2.6 4.6 + - - -
2365B ILE* 1.3 77.1 - - + +
2367B GLU* 1.3 63.0 + - + +
2369B ASP* 3.1 17.2 + - - +
2418B LYS* 5.1 6.8 + - - -
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Residues in contact with GLU2367 (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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2195B LYS* 2.8 56.0 + - - +
2363B SER* 2.7 20.0 + - - +
2364B TYR 2.7 9.0 + - - +
2366B GLU* 1.3 73.3 - - + +
2368B LEU* 1.3 60.3 + - + +
2369B ASP* 3.2 2.7 + - - +
2393B LYS* 5.3 2.4 + - - -
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Residues in contact with LEU2368 (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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2195B LYS* 3.9 15.0 - - - +
2198B LYS* 3.6 18.8 - - - +
2364B TYR* 3.0 40.4 + - + +
2367B GLU* 1.3 77.4 - - - +
2369B ASP* 1.3 70.3 + - - +
2370B ILE* 3.9 19.6 - - + +
2388B VAL* 5.6 2.2 - - + -
2389B LEU 3.3 24.9 - - - +
2390B ARG* 3.4 22.9 - - + -
2391B VAL* 3.2 20.3 - - + +
2393B LYS* 3.9 4.3 - - - -
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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