Contacts of the helix formed by residues 2532 - 2537 (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 THR2532 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2506B LEU* 3.7 5.9 - - - +
2530B PHE* 2.3 24.4 + - - +
2531B GLY 1.3 72.9 + - - -
2533B MET* 1.3 79.9 + - + +
2534B ASP* 3.4 24.0 - - + +
2535B ARG* 3.2 13.8 + - - +
2536B LEU* 3.1 18.2 + - - +
2581B MET* 3.3 16.2 - - + +
2582B GLU* 4.6 14.2 + - + +
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Residues in contact with MET2533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2506B LEU* 3.9 8.2 - - + +
2509B LEU* 5.1 7.6 - - + -
2510B LEU* 4.4 14.6 - - + -
2513B LEU* 5.4 4.7 - - + -
2532B THR* 1.3 74.1 - - - +
2534B ASP* 1.3 58.4 + - - +
2536B LEU* 2.6 46.6 + - - +
2537B LEU* 2.8 25.3 + - + +
2567B PHE* 3.4 31.4 - - + -
2571B VAL* 3.1 38.1 - - + -
2575B LYS* 6.1 1.1 - - - -
2581B MET* 3.0 35.0 + - + +
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Residues in contact with ASP2534 (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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2532B THR* 3.4 14.8 - - + +
2533B MET* 1.3 80.8 - - - +
2535B ARG* 1.3 60.2 + - - +
2537B LEU* 3.4 26.5 + - - +
2538B GLU* 3.5 19.4 + - - +
2575B LYS* 3.3 31.8 + - - -
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Residues in contact with ARG2535 (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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2529B ARG* 4.4 14.2 - - - +
2530B PHE* 3.0 45.9 - - + +
2532B THR* 3.2 13.1 + - - +
2533B MET 3.0 0.6 - - - -
2534B ASP* 1.3 77.1 - - - +
2536B LEU* 1.3 64.5 + - - +
2538B GLU* 3.3 21.8 + - - +
2539B ALA* 3.6 1.0 + - - -
2543B GLU* 2.9 39.4 + - - -
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Residues in contact with LEU2536 (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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2506B LEU* 6.4 0.2 - - + -
2510B LEU* 3.8 32.1 - - + -
2515B LEU* 4.8 3.6 - - + -
2526B LEU* 4.5 12.3 - - + -
2530B PHE* 3.1 43.3 - - + +
2532B THR 3.1 10.7 + - - +
2533B MET* 2.6 22.3 + - - +
2535B ARG* 1.3 68.1 - - - +
2537B LEU* 1.3 54.1 + - - +
2538B GLU 2.8 4.7 - - - -
2539B ALA* 2.5 35.6 + - + +
2544B LEU* 4.1 9.4 - - + -
2558B ILE* 5.3 0.9 - - + -
2562B LEU* 3.5 40.6 - - + +
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Residues in contact with LEU2537 (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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2533B MET* 2.8 28.4 + - + +
2534B ASP* 3.6 28.5 - - - +
2535B ARG 3.3 0.4 - - - -
2536B LEU* 1.3 76.5 - - - +
2538B GLU* 1.3 62.2 + - - +
2539B ALA 3.3 2.6 + - - +
2562B LEU* 3.4 37.5 - - + +
2563B LYS* 4.8 5.4 - - - +
2567B PHE* 4.2 23.1 - - + -
2568B ARG* 3.2 43.6 + - - +
2571B VAL* 4.6 12.1 - - + -
2575B LYS* 5.8 1.3 - - - +
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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