Contacts of the helix formed by residues 2551 - 2563 (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 GLY2551 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2545B LEU* 3.8 3.6 - - - -
2549B GLU 4.0 2.4 + - - -
2550B VAL* 1.3 73.5 - - - +
2552B GLU* 1.3 68.5 + - - -
2553B LEU* 2.8 4.8 + - - -
2554B THR* 2.9 13.8 + - - -
2555B ALA 2.8 20.1 + - - -
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Residues in contact with GLU2552 (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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2541B LEU* 4.5 3.2 - - + +
2545B LEU* 3.5 29.9 - - + +
2551B GLY* 1.3 68.5 - - - -
2553B LEU* 1.3 69.5 - - + +
2555B ALA* 3.1 2.3 - - - +
2556B ARG* 2.8 54.2 + - - +
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Residues in contact with LEU2553 (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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2419B GLU* 6.4 0.2 - - - -
2420B GLY 6.1 3.1 - - - +
2551B GLY 2.8 4.0 + - - -
2552B GLU* 1.3 88.5 - - + +
2554B THR* 1.3 67.8 + - + +
2555B ALA 3.0 1.3 - - - -
2556B ARG* 3.4 6.7 + - - +
2557B ALA* 2.9 24.1 + - - +
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Residues in contact with THR2554 (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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2516B PRO 4.3 9.4 - - - +
2517B GLY* 4.4 20.2 - - - +
2522B LEU* 5.7 2.8 - - - +
2549B GLU 5.1 0.7 + - - -
2550B VAL* 4.2 6.6 - - - +
2551B GLY* 2.9 27.8 + - - -
2553B LEU* 1.3 77.5 - - + +
2555B ALA* 1.3 51.2 + - - +
2557B ALA* 3.2 8.7 - - - +
2558B ILE* 2.8 42.8 + - - +
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Residues in contact with ALA2555 (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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2541B LEU* 3.9 11.7 - - + -
2544B LEU* 3.7 12.1 - - + +
2545B LEU* 3.3 31.4 - - + -
2550B VAL* 4.0 14.4 - - + -
2551B GLY 2.8 6.7 + - - +
2552B GLU 3.1 10.1 - - - +
2554B THR* 1.3 74.0 + - - +
2556B ARG* 1.3 60.4 + - - +
2557B ALA 2.9 3.6 - - - -
2558B ILE* 2.8 24.3 + - - +
2559B LEU* 2.9 11.1 + - - +
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Residues in contact with ARG2556 (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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2541B LEU* 3.4 38.9 - - + +
2552B GLU* 2.8 44.6 + - - +
2553B LEU* 4.2 5.9 - - - +
2555B ALA* 1.3 73.7 - - - +
2557B ALA* 1.3 61.2 + - - +
2559B LEU* 3.7 8.2 - - + +
2560B GLU* 3.0 29.4 + - + +
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Residues in contact with ALA2557 (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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2419B GLU* 4.1 25.1 - - + +
2516B PRO* 3.7 22.1 - - + +
2553B LEU 2.9 19.2 + - - +
2554B THR* 3.2 11.7 - - - +
2556B ARG* 1.3 75.7 - - - +
2558B ILE* 1.3 66.1 + - - +
2560B GLU* 3.4 7.0 + - - +
2561B THR* 3.0 24.9 + - - -
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Residues in contact with ILE2558 (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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2515B LEU* 5.0 12.1 - - + -
2516B PRO* 3.8 24.2 - - + +
2517B GLY 5.8 0.2 - - - -
2518B VAL* 5.0 5.2 - - + +
2522B LEU* 4.6 12.3 - - + -
2526B LEU* 4.1 26.2 - - + -
2536B LEU* 5.3 2.7 - - + -
2544B LEU* 3.8 15.9 - - + -
2550B VAL* 4.9 10.3 - - + -
2554B THR* 2.8 21.7 + - - +
2555B ALA* 2.8 7.9 + - - +
2557B ALA* 1.3 73.6 - - - +
2559B LEU* 1.3 66.6 + - - +
2561B THR* 2.9 4.6 + - - -
2562B LEU* 2.8 52.2 + - + +
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Residues in contact with LEU2559 (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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2539B ALA 4.4 10.8 - - - +
2540B SER* 4.2 2.2 - - - -
2541B LEU* 3.3 46.7 - - + +
2544B LEU* 4.0 8.3 - - + +
2555B ALA 2.9 11.0 + - - +
2556B ARG* 3.7 14.8 - - + +
2558B ILE* 1.3 76.7 - - - +
2560B GLU* 1.3 73.7 + - - +
2562B LEU* 3.3 8.8 + - - +
2563B LYS* 3.1 34.3 + - + +
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Residues in contact with GLU2560 (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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2417B VAL* 6.1 5.2 - - + -
2419B GLU* 6.1 0.4 - - - +
2426B PRO* 6.2 4.3 - - + -
2556B ARG* 3.0 21.7 + - + +
2557B ALA* 3.5 7.6 - - - +
2558B ILE 3.2 0.2 - - - -
2559B LEU* 1.3 85.8 - - - +
2561B THR* 1.3 60.5 + - - +
2563B LYS* 3.5 11.0 + - - +
2564B ASP* 3.5 12.5 + - - +
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Residues in contact with THR2561 (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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2426B PRO* 4.6 14.4 + - - +
2428B PRO* 4.0 26.0 - - + -
2515B LEU* 4.6 17.3 - - + -
2516B PRO* 3.5 26.4 - - + +
2557B ALA 3.0 14.0 + - - -
2558B ILE* 2.9 8.0 + - - -
2560B GLU* 1.3 72.9 - - - +
2562B LEU* 1.3 67.0 + - - +
2563B LYS 3.0 3.6 + - - -
2564B ASP* 3.1 18.3 + - + +
2567B PHE* 3.5 13.3 - - + +
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Residues in contact with LEU2562 (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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2515B LEU* 4.4 13.7 - - + -
2533B MET* 5.3 0.2 - - - -
2536B LEU* 3.5 53.6 - - + +
2537B LEU* 3.4 22.8 - - + +
2539B ALA* 4.5 7.2 - - + +
2544B LEU* 4.8 0.4 - - + -
2558B ILE* 2.8 39.6 + - + +
2559B LEU* 3.3 8.9 + - - +
2561B THR* 1.3 77.7 - - - +
2563B LYS* 1.3 59.8 + - + +
2564B ASP 3.8 0.2 + - - -
2567B PHE* 3.9 25.0 - - + -
2568B ARG* 3.1 24.0 + - - +
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Residues in contact with LYS2563 (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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2537B LEU 4.8 4.3 - - - +
2559B LEU* 3.1 27.4 + - + +
2560B GLU* 4.0 6.7 - - - +
2561B THR 3.0 1.2 - - - -
2562B LEU* 1.3 79.5 - - + +
2564B ASP* 1.3 60.7 + - - +
2565B PRO* 3.6 6.1 - - - +
2568B ARG* 3.4 29.9 + - - +
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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