Contacts of the helix formed by residues 2580 - 2593 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2520F LEU* 5.1 11.2 - - + -
2570F PHE* 4.4 23.0 - - + -
2579F MET* 1.3 72.4 - - - +
2581F ASP* 1.3 63.9 + - - +
2583F MET* 3.4 11.8 + - - +
2584F LEU* 3.4 23.6 - - + +
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Residues in contact with ASP2581 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2579F MET* 3.3 1.2 - - - +
2580F VAL* 1.3 80.1 - - - +
2582F SER* 1.3 60.2 + - - +
2584F LEU* 3.3 20.0 + - - +
2585F HIS* 3.9 4.2 + - - +
2623F LEU* 3.8 42.3 - - + +
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Residues in contact with SER2582 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2579F MET* 3.5 23.2 + - - +
2580F VAL 3.3 0.4 - - - -
2581F ASP* 1.3 76.3 - - - +
2583F MET* 1.3 63.9 + - - +
2584F LEU 3.2 0.2 - - - -
2585F HIS* 3.3 16.9 + - - +
2586F THR* 3.6 11.8 + - - +
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Residues in contact with MET2583 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2524F ASP* 6.0 6.1 - - + -
2579F MET 3.4 11.4 + - - +
2580F VAL* 3.7 12.3 - - - +
2581F ASP 3.2 1.0 - - - -
2582F SER* 1.3 77.7 - - - +
2584F LEU* 1.3 66.0 + - + +
2586F THR* 3.3 22.1 - - + +
2587F VAL* 3.7 9.4 + - - +
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Residues in contact with LEU2584 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2570F PHE* 5.0 14.8 - - + -
2580F VAL 3.4 17.3 - - - +
2581F ASP* 3.3 11.4 + - - +
2582F SER 3.2 1.0 - - - -
2583F MET* 1.3 79.2 - - + +
2585F HIS* 1.3 64.6 + - - +
2587F VAL* 3.7 11.6 + - + +
2588F TYR* 3.7 11.6 + - - +
2607F CYS* 6.5 0.2 - - - -
2608F LEU* 3.9 27.2 - - + +
2611F LEU* 4.6 26.2 - - + +
2615F ILE* 6.3 1.6 - - + -
2620F LEU* 6.2 4.3 - - + -
2623F LEU* 6.0 2.0 - - + -
2624F LEU* 5.3 15.7 - - + +
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Residues in contact with HIS2585 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2581F ASP 3.9 4.6 + - - +
2582F SER* 3.3 14.4 + - - +
2583F MET 3.3 1.0 - - - -
2584F LEU* 1.3 78.1 - - - +
2586F THR* 1.3 63.4 + - - +
2587F VAL 3.2 0.6 + - - -
2588F TYR* 3.3 8.2 + - - +
2589F ARG* 3.3 18.7 + - - +
2623F LEU* 6.3 1.1 - - + -
2627F LEU* 3.8 30.3 - - + -
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Residues in contact with THR2586 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2582F SER 3.6 7.2 + - - +
2583F MET* 3.3 25.8 - - + +
2585F HIS* 1.3 75.4 - - - +
2587F VAL* 1.3 65.0 + - + +
2589F ARG* 3.7 9.6 - - - +
2590F LEU* 3.4 31.8 + - - +
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Residues in contact with VAL2587 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2560F LEU* 6.0 3.8 - - + -
2583F MET 3.7 10.0 + - - +
2584F LEU* 3.9 7.2 - - + +
2585F HIS 3.2 0.8 - - - -
2586F THR* 1.3 82.9 - - - +
2588F TYR* 1.3 62.3 + - - +
2590F LEU* 3.5 7.9 + - - +
2591F SER* 3.4 14.7 + - - -
2604F ILE* 3.8 17.2 - - + +
2607F CYS* 5.3 10.1 - - + -
2608F LEU* 3.8 25.9 - - + +
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Residues in contact with TYR2588 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2584F LEU 3.7 8.1 + - - +
2585F HIS* 3.3 11.0 + - - +
2587F VAL* 1.3 77.0 - - - +
2589F ARG* 1.3 66.9 + - - +
2591F SER* 3.2 10.8 + - - -
2592F ARG* 3.1 34.3 + - + +
2608F LEU* 4.4 20.7 - - + +
2628F VAL* 3.5 37.7 - - + +
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Residues in contact with ARG2589 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2585F HIS 3.3 12.6 + - - +
2586F THR* 3.7 13.7 - - - +
2587F VAL 3.3 0.6 - - - -
2588F TYR* 1.3 81.0 - - - +
2590F LEU* 1.3 64.8 + - + +
2591F SER 3.5 0.2 + - - -
2592F ARG* 3.6 5.8 + - - +
2593F GLY* 3.5 15.4 + - - -
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Residues in contact with LEU2590 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2552F ASN* 5.1 12.9 + - - +
2555F LEU* 5.1 15.3 - - + -
2586F THR* 3.4 22.5 + - - +
2587F VAL* 3.5 8.7 + - - +
2588F TYR 3.3 0.4 - - - -
2589F ARG* 1.3 79.1 - - + +
2591F SER* 1.3 62.4 + - - +
2593F GLY* 3.6 13.6 + - - +
2596F LEU* 5.2 3.3 - - - +
2604F ILE* 4.1 22.6 - - + +
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Residues in contact with SER2591 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2587F VAL 3.4 6.6 + - - -
2588F TYR* 3.2 20.0 + - - -
2590F LEU* 1.3 78.3 - - - +
2592F ARG* 1.3 62.3 + - - +
2593F GLY 3.4 7.3 + - - +
2601F ARG* 6.0 0.4 - - - +
2604F ILE* 3.7 27.1 - - - +
2605F GLU* 5.6 2.7 - - - -
2608F LEU* 5.2 5.4 - - - -
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Residues in contact with ARG2592 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2588F TYR* 3.1 33.5 + - + +
2589F ARG* 4.0 6.5 - - - +
2590F LEU 3.4 0.4 - - - -
2591F SER* 1.3 73.8 - - - +
2593F GLY* 1.3 62.8 + - - +
2594F ARG* 3.6 2.6 + - - +
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Residues in contact with GLY2593 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2589F ARG 3.5 11.0 + - - -
2590F LEU* 3.6 11.0 + - - +
2591F SER 3.2 9.9 - - - +
2592F ARG* 1.3 79.2 - - - +
2594F ARG* 1.3 62.6 + - - -
2595F SER* 3.4 7.8 + - - -
2596F LEU* 4.6 7.7 - - - +
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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