Contacts of the helix formed by residues 2519 - 2531 (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 GLY2519 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2511B TYR* 4.0 15.3 - - - -
2517B GLY 3.7 3.0 + - - -
2518B VAL* 1.3 74.5 - - - +
2520B GLU* 1.3 58.9 + - - -
2521B VAL* 3.3 5.6 - - - +
2522B LEU* 3.6 7.6 - - - +
2523B ALA* 2.7 33.3 + - - +
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Residues in contact with GLU2520 (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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2445B LYS* 2.7 50.4 + - - +
2511B TYR* 4.1 25.1 + - + +
2519B GLY* 1.3 71.4 - - - -
2521B VAL* 1.3 63.4 + - - +
2523B ALA* 3.7 4.5 - - - +
2524B ARG* 3.3 47.5 + - - +
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Residues in contact with VAL2521 (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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2519B GLY* 4.9 3.6 - - - -
2520B GLU* 1.3 77.2 - - - +
2522B LEU* 1.3 81.7 + - + +
2524B ARG* 3.4 13.9 + - - +
2525B ASN* 2.8 41.5 + - - +
2548B GLU* 5.2 6.5 - - - +
2549B GLU* 5.6 10.3 - - + -
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Residues in contact with LEU2522 (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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2517B GLY 3.5 20.0 - - - +
2518B VAL* 3.6 12.1 - - + -
2519B GLY 3.3 11.1 + - - +
2521B VAL* 1.3 85.0 - - + +
2523B ALA* 1.3 67.3 + - - +
2525B ASN* 2.8 19.7 + - - +
2526B LEU* 2.9 48.1 + - + -
2547B VAL* 4.9 0.7 - - + -
2548B GLU 4.8 0.9 - - - +
2549B GLU* 3.3 33.2 - - + +
2550B VAL* 3.5 18.2 - - + -
2554B THR* 5.7 3.1 - - - +
2558B ILE* 4.6 7.9 - - + -
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Residues in contact with ALA2523 (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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2507B GLU* 3.5 26.5 - - - +
2510B LEU* 4.0 3.7 - - + +
2511B TYR* 3.8 20.9 - - + +
2518B VAL* 3.4 11.3 - - + +
2519B GLY 2.7 22.0 + - - +
2520B GLU* 3.7 4.9 - - - +
2522B LEU* 1.3 71.0 - - - +
2524B ARG* 1.3 65.2 + - - +
2526B LEU* 2.9 16.8 + - - +
2527B ALA* 3.1 15.2 + - - +
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Residues in contact with ARG2524 (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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2507B GLU* 4.3 19.2 - - + +
2520B GLU* 3.3 40.4 + - - +
2521B VAL* 3.5 17.8 - - - +
2522B LEU 3.2 0.2 - - - -
2523B ALA* 1.3 77.7 - - - +
2525B ASN* 1.3 65.3 + - - +
2527B ALA* 4.0 1.2 - - - +
2528B ARG* 2.9 69.8 + - - +
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Residues in contact with ASN2525 (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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2521B VAL* 2.8 36.8 + - - +
2522B LEU* 2.8 14.6 + - - +
2524B ARG* 1.3 76.1 - - - +
2526B LEU* 1.3 65.2 + - - +
2528B ARG* 3.5 9.1 + - - +
2529B ARG* 3.0 22.5 + - - +
2547B VAL* 3.5 21.8 - - + +
2548B GLU* 3.5 33.7 + - + +
2549B GLU* 5.0 0.8 - - - +
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Residues in contact with LEU2526 (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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2510B LEU* 3.6 15.0 - - + -
2515B LEU* 4.9 9.4 - - + -
2518B VAL* 3.7 29.4 - - + -
2522B LEU* 2.9 29.7 + - + +
2523B ALA 2.9 8.6 + - - +
2525B ASN* 1.3 75.3 - - - +
2527B ALA* 1.3 55.4 + - - +
2529B ARG* 2.6 26.9 + - - +
2530B PHE* 3.0 24.4 + - + -
2536B LEU* 4.5 16.8 - - + -
2544B LEU* 5.2 4.0 - - + -
2547B VAL* 3.8 23.3 - - + -
2550B VAL* 4.3 3.4 - - + -
2558B ILE* 4.1 19.1 - - + -
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Residues in contact with ALA2527 (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* 3.5 33.0 - - + -
2507B GLU* 3.5 18.6 - - + +
2510B LEU* 3.3 21.3 - - + +
2523B ALA 3.1 3.1 + - - +
2524B ARG 4.4 0.7 - - - +
2526B LEU* 1.3 79.1 - - - +
2528B ARG* 1.3 56.8 + - - +
2530B PHE* 4.5 2.9 - - - +
2531B GLY* 2.9 29.4 + - - -
2583B SER* 3.6 10.6 + - - -
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Residues in contact with ARG2528 (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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2507B GLU* 5.6 6.5 - - - +
2524B ARG* 2.9 59.2 + - - +
2525B ASN* 3.7 8.4 + - - +
2526B LEU 3.0 0.2 + - - -
2527B ALA* 1.3 78.4 - - - +
2529B ARG* 1.3 59.5 + - - +
2531B GLY* 4.4 1.8 + - - -
2583B SER* 4.9 6.1 - - - -
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Residues in contact with ARG2529 (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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2525B ASN 3.0 16.4 + - - +
2526B LEU 2.6 12.9 + - - +
2528B ARG* 1.3 73.5 - - - +
2530B PHE* 1.3 87.0 + - + +
2531B GLY 3.6 0.2 - - - -
2535B ARG* 4.4 11.3 - - - +
2543B GLU* 3.8 26.1 + - - +
2546B GLU* 3.7 27.5 + - - +
2547B VAL* 4.1 13.9 - - + +
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Residues in contact with PHE2530 (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* 5.1 0.7 - - + -
2526B LEU* 3.0 28.3 + - + +
2527B ALA* 5.2 1.3 - - - -
2529B ARG* 1.3 115.0 - - + +
2531B GLY* 1.3 50.5 + - - +
2532B THR* 2.3 25.1 + - - +
2535B ARG* 3.0 45.0 - - + +
2536B LEU* 3.1 43.1 - - + +
2539B ALA* 4.5 2.7 - - + -
2543B GLU* 3.9 33.0 - - + -
2544B LEU* 3.7 23.8 - - + -
2547B VAL* 4.2 9.2 - - + -
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Residues in contact with GLY2531 (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* 3.1 6.7 - - - +
2527B ALA 2.9 17.4 + - - -
2528B ARG 4.4 2.1 + - - -
2529B ARG 3.6 2.0 - - - +
2530B PHE* 1.3 72.1 - - - +
2532B THR* 1.3 60.2 + - - -
2582B GLU* 3.3 7.3 - - - +
2583B SER* 3.1 32.8 + - - -
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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