Contacts of the helix formed by residues 2564 - 2577 (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 ASP2564 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2414B HIS* 2.7 35.9 + - - -
2426B PRO 5.0 1.0 - - - +
2428B PRO* 4.3 11.4 - - + +
2560B GLU 3.5 10.3 + - - +
2561B THR* 3.1 17.4 + - - +
2562B LEU 3.4 0.2 - - - -
2563B LYS* 1.3 76.3 - - - +
2565B PRO* 1.3 78.8 - - - +
2566B ALA* 2.5 42.8 + - - +
2567B PHE* 2.9 18.0 + - + +
2568B ARG* 3.0 12.6 + - - +
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Residues in contact with PRO2565 (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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2414B HIS* 6.4 0.4 - - + -
2563B LYS 3.6 6.8 - - - +
2564B ASP* 1.3 88.1 - - - +
2566B ALA* 1.3 65.4 + - + +
2568B ARG* 3.2 10.3 + - + +
2569B ASP* 2.9 24.3 + - - +
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Residues in contact with ALA2566 (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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2414B HIS* 5.5 1.1 - - + -
2427B ASN* 3.1 32.8 - - - +
2428B PRO* 4.2 2.7 - - + -
2429B LEU* 3.5 24.8 - - + +
2564B ASP* 2.5 20.4 + - - +
2565B PRO* 1.3 74.0 - - + +
2567B PHE* 1.3 61.6 + - - +
2569B ASP* 3.3 9.3 - - - +
2570B LEU* 3.2 14.0 + - - +
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Residues in contact with PHE2567 (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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2428B PRO* 4.1 27.9 - - + +
2510B LEU* 6.0 0.2 - - + -
2513B LEU* 3.8 28.3 - - + -
2515B LEU* 3.8 26.0 - - + -
2533B MET* 3.4 33.9 - - + -
2537B LEU* 4.2 6.1 - - + -
2561B THR* 3.5 24.7 - - + +
2562B LEU* 3.9 26.9 - - + -
2564B ASP* 2.9 12.7 + - + +
2566B ALA* 1.3 70.7 - - - +
2568B ARG* 1.3 60.8 + - - +
2569B ASP 3.0 1.6 - - - -
2570B LEU* 2.6 34.2 + - + +
2571B VAL* 2.8 23.0 + - + +
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Residues in contact with ARG2568 (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* 3.2 52.6 + - - +
2538B GLU* 4.4 10.5 + - - -
2562B LEU 3.1 20.4 + - - +
2563B LYS* 3.4 34.6 + - - +
2564B ASP 3.3 17.5 - - - +
2565B PRO* 3.3 11.9 - - + +
2567B PHE* 1.3 77.2 - - - +
2569B ASP* 1.3 56.6 + - - +
2571B VAL* 3.2 11.3 - - - +
2572B ARG* 3.0 50.6 + - - +
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Residues in contact with ASP2569 (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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2429B LEU* 4.4 5.4 - - + +
2565B PRO 2.9 12.6 + - - +
2566B ALA* 3.3 13.7 - - - +
2568B ARG* 1.3 76.5 - - - +
2570B LEU* 1.3 61.5 + - - +
2572B ARG* 3.1 18.5 + - - +
2573B ARG* 2.7 66.6 + - - +
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Residues in contact with LEU2570 (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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2428B PRO* 5.0 8.5 - - + +
2429B LEU* 4.0 13.9 - - + -
2468B ASP* 3.4 35.0 - - + +
2469B VAL* 3.6 25.6 - - + -
2470B ALA* 4.2 3.4 - - + +
2513B LEU* 3.5 31.4 - - + -
2566B ALA 3.2 7.9 + - - +
2567B PHE* 2.6 22.7 + - + +
2569B ASP* 1.3 74.4 + - - +
2571B VAL* 1.3 56.8 + - - +
2572B ARG 2.9 5.2 + - - -
2573B ARG* 3.3 11.3 + - - +
2574B LEU* 3.0 33.3 + - + +
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Residues in contact with VAL2571 (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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2509B LEU* 5.7 0.9 - - + -
2513B LEU* 6.2 0.9 - - + -
2533B MET* 3.1 47.8 - - + -
2537B LEU* 4.6 13.5 - - + -
2567B PHE* 2.8 33.0 + - + +
2568B ARG* 3.2 24.5 - - - +
2570B LEU* 1.3 74.4 - - - +
2572B ARG* 1.3 61.9 + - - +
2574B LEU* 4.1 12.3 - - + -
2575B LYS* 3.6 7.7 - - - +
2581B MET* 3.3 24.4 - - + +
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Residues in contact with ARG2572 (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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2568B ARG* 3.0 36.5 + - - +
2569B ASP* 3.2 24.3 + - - +
2570B LEU 2.9 0.6 - - - -
2571B VAL* 1.3 76.2 - - - +
2573B ARG* 1.3 59.3 + - + +
2575B LYS* 2.6 43.0 + - + +
2576B GLU* 2.8 33.4 + - + +
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Residues in contact with ARG2573 (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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2429B LEU* 3.9 12.7 - - - +
2467B ARG* 4.7 9.7 - - - +
2468B ASP* 2.8 42.0 + - - -
2470B ALA* 3.7 16.7 - - + +
2471B ASP* 4.5 10.5 + - - -
2474B HIS* 5.2 12.7 + - - +
2569B ASP* 2.7 36.2 + - - +
2570B LEU* 3.7 15.3 - - - +
2572B ARG* 1.3 81.6 - - + +
2574B LEU* 1.3 51.4 + - - +
2576B GLU* 2.9 23.6 + - - +
2577B ALA* 2.6 38.3 + - - +
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Residues in contact with LEU2574 (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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2441B TYR* 4.2 12.8 - - + +
2469B VAL* 3.6 17.5 - - + -
2470B ALA* 3.3 38.1 - - + +
2473B TYR* 4.7 2.5 - - + -
2509B LEU* 4.2 14.8 - - + -
2513B LEU* 4.0 27.1 - - + -
2570B LEU* 3.0 22.1 + - + +
2571B VAL* 4.3 9.0 - - + +
2573B ARG* 1.3 76.4 - - - +
2575B LYS* 1.3 59.4 + - - +
2577B ALA* 3.6 5.0 + - - -
2578B GLY 3.3 3.1 + - - -
2579B VAL* 2.9 40.2 + - + +
2581B MET* 3.7 11.9 - - + -
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Residues in contact with LYS2575 (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* 6.1 1.3 - - - -
2534B ASP* 3.3 33.0 + - - -
2537B LEU* 5.8 1.4 - - - +
2571B VAL* 3.6 9.8 + - - +
2572B ARG* 2.6 28.4 + - + +
2574B LEU* 1.3 72.1 - - - +
2576B GLU* 1.3 63.6 + - + +
2577B ALA 3.2 0.2 - - - -
2578B GLY* 3.3 10.2 + - - -
2579B VAL 4.1 4.3 - - - +
2581B MET* 3.3 32.1 - - + +
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Residues in contact with GLU2576 (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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2474B HIS* 5.6 8.1 + - + -
2476B ARG* 5.4 2.1 + - - -
2572B ARG* 2.8 36.8 + - + +
2573B ARG* 3.4 26.4 - - - +
2575B LYS* 1.3 79.4 - - + +
2577B ALA* 1.3 59.0 + - - +
2578B GLY* 3.1 4.7 + - - -
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Residues in contact with ALA2577 (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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2470B ALA* 4.8 4.9 - - + +
2473B TYR* 3.8 30.5 - - + +
2474B HIS* 4.5 18.4 - - + +
2476B ARG* 5.0 8.5 + - - +
2502B LYS* 3.4 26.9 + - - -
2573B ARG 2.6 19.8 + - - +
2574B LEU* 3.9 9.4 - - - +
2575B LYS 3.2 0.2 - - - -
2576B GLU* 1.3 74.2 - - - +
2578B GLY* 1.3 56.0 + - - +
2579B VAL 3.5 0.6 + - - -
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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