Contacts of the helix formed by residues 2580 - 2593 (chain B) in PDB entry 6X34
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 VAL2580 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2520B LEU* 5.1 11.2 - - + -
2570B PHE* 4.4 22.8 - - + -
2579B MET* 1.3 73.8 - - - +
2581B ASP* 1.3 64.5 + - - +
2583B MET* 3.4 11.8 + - - +
2584B LEU* 3.4 23.9 - - - +
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Residues in contact with ASP2581 (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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2579B MET* 3.3 1.2 - - - +
2580B VAL* 1.3 79.3 - - - +
2582B SER* 1.3 59.8 + - - +
2584B LEU* 3.3 19.2 + - - +
2585B HIS* 3.9 4.9 + - - +
2623B LEU* 3.8 43.7 - - + +
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Residues in contact with SER2582 (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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2579B MET* 3.5 22.2 + - - +
2580B VAL 3.3 0.2 - - - -
2581B ASP* 1.3 76.6 - - - +
2583B MET* 1.3 62.9 + - - +
2585B HIS* 3.3 17.6 + - - +
2586B THR* 3.6 12.0 + - - +
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Residues in contact with MET2583 (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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2524B ASP* 6.0 6.1 - - + -
2579B MET 3.4 11.4 + - - +
2580B VAL* 3.7 13.2 - - - +
2581B ASP 3.2 0.8 - - - -
2582B SER* 1.3 78.5 - - - +
2584B LEU* 1.3 65.6 + - + +
2586B THR* 3.3 22.6 - - + +
2587B VAL* 3.7 10.2 + - - +
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Residues in contact with LEU2584 (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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2570B PHE* 5.0 15.3 - - + -
2580B VAL 3.4 16.6 - - - +
2581B ASP* 3.3 11.3 + - - +
2582B SER 3.2 0.8 - - - -
2583B MET* 1.3 80.3 - - + +
2585B HIS* 1.3 63.5 + - - +
2586B THR 3.5 0.2 - - - -
2587B VAL* 3.7 11.3 + - + +
2588B TYR* 3.7 11.6 + - - +
2607B CYS* 6.5 0.2 - - - -
2608B LEU* 3.9 28.2 - - + +
2611B LEU* 4.6 25.8 - - + +
2615B ILE* 6.3 1.8 - - + -
2620B LEU* 6.2 4.3 - - + -
2623B LEU* 6.0 1.6 - - + -
2624B LEU* 5.3 15.7 - - + +
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Residues in contact with HIS2585 (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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2581B ASP 3.9 3.9 + - - +
2582B SER* 3.3 14.6 + - - +
2583B MET 3.3 0.6 - - - -
2584B LEU* 1.3 77.2 - - - +
2586B THR* 1.3 63.9 + - - +
2587B VAL 3.2 0.2 - - - -
2588B TYR* 3.3 8.6 + - - +
2589B ARG* 3.3 18.9 + - - +
2623B LEU* 6.3 1.3 - - + -
2627B LEU* 3.8 29.6 - - + -
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Residues in contact with THR2586 (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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2582B SER 3.6 7.4 + - - +
2583B MET* 3.3 26.9 - - + +
2585B HIS* 1.3 76.2 - - - +
2587B VAL* 1.3 63.1 + - + +
2588B TYR 3.4 0.2 - - - -
2589B ARG* 3.5 9.2 + - - +
2590B LEU* 3.4 33.1 + - - +
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Residues in contact with VAL2587 (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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2560B LEU* 6.0 3.6 - - + -
2583B MET 3.7 9.8 + - - +
2584B LEU* 3.9 7.6 - - + +
2585B HIS 3.2 1.0 - - - -
2586B THR* 1.3 81.0 - - + +
2588B TYR* 1.3 62.2 + - - +
2590B LEU* 3.5 8.1 + - - +
2591B SER* 3.4 14.6 + - - -
2604B ILE* 3.8 17.6 - - + +
2607B CYS* 5.3 10.1 - - + -
2608B LEU* 3.8 26.0 - - + +
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Residues in contact with TYR2588 (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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2584B LEU 3.7 8.1 + - - +
2585B HIS* 3.3 10.9 + - - +
2587B VAL* 1.3 76.7 - - - +
2589B ARG* 1.3 66.7 + - - +
2590B LEU 3.3 0.2 - - - -
2591B SER* 3.2 11.4 + - - -
2592B ARG* 3.1 34.4 + - + +
2608B LEU* 4.4 21.5 - - + +
2628B VAL* 3.5 37.9 - - + +
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Residues in contact with ARG2589 (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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2585B HIS 3.3 12.6 + - - +
2586B THR* 3.7 13.7 - - - +
2587B VAL 3.3 0.8 - - - -
2588B TYR* 1.3 81.1 - - - +
2590B LEU* 1.3 64.9 + - + +
2591B SER 3.5 0.2 + - - -
2592B ARG* 3.6 6.4 + - - +
2593B GLY* 3.5 15.6 + - - -
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Residues in contact with LEU2590 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2552B ASN* 5.1 13.7 + - - +
2555B LEU* 5.1 15.3 - - + -
2586B THR* 3.4 22.6 + - - +
2587B VAL* 3.5 8.5 + - - +
2588B TYR 3.3 0.4 - - - -
2589B ARG* 1.3 79.9 - - + +
2591B SER* 1.3 62.5 + - - +
2593B GLY* 3.6 13.7 + - - +
2596B LEU* 5.2 2.8 - - - +
2604B ILE* 4.1 22.8 - - + +
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Residues in contact with SER2591 (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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2587B VAL 3.4 5.7 + - - -
2588B TYR* 3.2 20.3 + - - -
2590B LEU* 1.3 78.3 - - - +
2592B ARG* 1.3 63.2 + - - +
2593B GLY 3.4 7.6 + - - +
2601B ARG* 6.0 0.4 - - - +
2604B ILE* 3.7 28.4 - - - +
2605B GLU* 5.6 2.7 - - - -
2608B LEU* 5.2 4.9 - - - -
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Residues in contact with ARG2592 (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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2588B TYR* 3.1 32.9 + - + +
2589B ARG* 4.0 7.0 - - - +
2590B LEU 3.4 0.2 - - - -
2591B SER* 1.3 74.8 - - - +
2593B GLY* 1.3 64.9 + - - +
2594B ARG* 3.6 2.6 + - - +
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Residues in contact with GLY2593 (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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2589B ARG 3.5 11.5 + - - -
2590B LEU* 3.6 10.6 + - - +
2591B SER 3.2 10.2 - - - +
2592B ARG* 1.3 80.5 - - - +
2594B ARG* 1.3 62.5 + - - -
2595B SER* 3.4 7.3 + - - -
2596B LEU* 4.6 7.8 - - - +
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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