Contacts of the helix formed by residues 2580 - 2593 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2520D LEU* 5.1 11.7 - - + -
2570D PHE* 4.4 22.8 - - + -
2579D MET* 1.3 73.4 - - - +
2581D ASP* 1.3 64.4 + - - +
2583D MET* 3.4 11.6 + - - +
2584D LEU* 3.4 23.2 - - - +
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Residues in contact with ASP2581 (chain D).
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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2579D MET* 3.3 1.2 - - - +
2580D VAL* 1.3 80.1 - - - +
2582D SER* 1.3 60.0 + - - +
2584D LEU* 3.3 20.1 + - - +
2585D HIS* 3.9 4.5 + - - +
2623D LEU* 3.8 42.7 - - + +
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Residues in contact with SER2582 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2579D MET* 3.5 22.4 + - - +
2580D VAL 3.4 0.4 - - - -
2581D ASP* 1.3 77.3 - - - +
2583D MET* 1.3 63.3 + - - +
2585D HIS* 3.3 17.2 + - - +
2586D THR* 3.6 11.8 + - - +
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Residues in contact with MET2583 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2524D ASP* 6.0 6.3 - - + -
2579D MET 3.4 11.0 + - - +
2580D VAL* 3.7 13.2 - - - +
2581D ASP 3.2 0.8 - - - -
2582D SER* 1.3 77.5 - - - +
2584D LEU* 1.3 64.8 + - + +
2585D HIS 3.3 0.2 - - - -
2586D THR* 3.3 23.5 - - + +
2587D VAL* 3.7 9.9 + - - +
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Residues in contact with LEU2584 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2570D PHE* 5.0 15.3 - - + -
2580D VAL 3.4 17.7 - - - +
2581D ASP* 3.3 11.6 + - - +
2582D SER 3.2 1.0 - - - -
2583D MET* 1.3 79.0 - - + +
2585D HIS* 1.3 63.1 + - - +
2587D VAL* 3.7 11.5 + - + +
2588D TYR* 3.7 12.0 + - - +
2607D CYS* 6.5 0.7 - - - -
2608D LEU* 3.9 28.2 - - + +
2611D LEU* 4.6 26.0 - - + +
2615D ILE* 6.3 1.6 - - + -
2620D LEU* 6.2 4.0 - - + -
2623D LEU* 6.0 1.6 - - + -
2624D LEU* 5.3 15.7 - - + -
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Residues in contact with HIS2585 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2581D ASP 3.9 4.5 + - - +
2582D SER* 3.3 14.1 + - - +
2583D MET 3.3 0.8 - - - -
2584D LEU* 1.3 78.1 - - - +
2586D THR* 1.3 63.5 + - - +
2588D TYR* 3.3 8.8 + - - +
2589D ARG* 3.3 18.9 + - - +
2623D LEU* 6.3 1.6 - - + -
2627D LEU* 3.8 28.9 - - + -
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Residues in contact with THR2586 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2582D SER 3.6 7.0 + - - +
2583D MET* 3.3 26.7 - - + +
2585D HIS* 1.3 75.9 - - - +
2587D VAL* 1.3 62.6 + - - +
2589D ARG* 3.5 10.2 + - - +
2590D LEU* 3.4 32.2 + - - +
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Residues in contact with VAL2587 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2560D LEU* 6.0 4.3 - - + -
2583D MET 3.7 10.0 + - - +
2584D LEU* 3.9 7.2 - - + +
2585D HIS 3.2 1.0 - - - -
2586D THR* 1.3 82.7 - - + +
2588D TYR* 1.3 60.9 + - - +
2590D LEU* 3.5 7.4 + - - +
2591D SER* 3.4 14.9 + - - -
2604D ILE* 3.8 17.3 - - + +
2607D CYS* 5.3 10.3 - - + -
2608D LEU* 3.8 25.4 - - + -
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Residues in contact with TYR2588 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2584D LEU 3.7 8.7 + - - +
2585D HIS* 3.3 10.1 + - - +
2587D VAL* 1.3 78.0 - - - +
2589D ARG* 1.3 66.2 + - - +
2591D SER* 3.2 10.9 + - - -
2592D ARG* 3.1 34.4 + - + +
2608D LEU* 4.4 21.5 - - + +
2628D VAL* 3.5 37.3 - - + +
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Residues in contact with ARG2589 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2585D HIS 3.3 12.8 + - - +
2586D THR* 3.7 13.2 - - - +
2587D VAL 3.3 0.8 - - - -
2588D TYR* 1.3 81.0 - - - +
2590D LEU* 1.3 65.4 + - + +
2591D SER 3.5 0.3 + - - -
2592D ARG* 3.6 5.7 + - - +
2593D GLY* 3.5 15.8 + - - -
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Residues in contact with LEU2590 (chain D).
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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2552D ASN* 5.1 12.7 + - - +
2555D LEU* 5.1 15.3 - - + -
2586D THR* 3.4 22.7 + - - +
2587D VAL* 4.0 8.7 - - - +
2588D TYR 3.3 0.4 - - - -
2589D ARG* 1.3 80.1 - - + +
2591D SER* 1.3 62.9 + - - +
2593D GLY* 3.6 13.3 + - - +
2596D LEU* 5.2 3.3 - - - +
2604D ILE* 4.1 23.6 - - + +
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Residues in contact with SER2591 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2587D VAL 3.4 6.2 + - - -
2588D TYR* 3.2 20.4 + - - -
2590D LEU* 1.3 78.1 - - - +
2592D ARG* 1.3 64.2 + - - +
2593D GLY 3.4 7.8 + - - +
2601D ARG* 6.0 0.6 - - - +
2604D ILE* 3.7 27.5 - - - +
2605D GLU* 5.6 2.7 - - - -
2608D LEU* 5.2 5.4 - - - -
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Residues in contact with ARG2592 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2588D TYR* 3.1 33.1 + - + +
2589D ARG* 4.0 7.2 - - - +
2590D LEU 3.4 0.4 - - - -
2591D SER* 1.3 75.6 - - - +
2593D GLY* 1.3 64.2 + - - +
2594D ARG* 3.6 2.4 + - - +
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Residues in contact with GLY2593 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2589D ARG 3.5 10.5 + - - -
2590D LEU* 3.6 10.7 + - - +
2591D SER 3.2 10.0 - - - +
2592D ARG* 1.3 80.6 - - - +
2594D ARG* 1.3 61.8 + - - -
2595D SER* 3.4 7.3 + - - -
2596D LEU* 4.6 8.0 - - - +
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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