Contacts of the helix formed by residues 2582 - 2595 (chain B) in PDB entry 5KJH
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 ASP2582 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311B ARG* 5.7 1.0 - - + +
2580B ILE* 3.9 15.9 - - + +
2581B ASP* 1.3 73.0 + - - +
2583B SER* 1.3 60.7 + - - +
2584B TRP* 3.2 8.1 - - - +
2585B LEU* 3.0 21.6 + - + +
2586B LEU* 2.8 39.2 + - + +
2616B ARG* 4.2 23.0 - - - +
2618B HIS* 3.4 27.0 + - + +
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Residues in contact with SER2583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 3.8 31.2 - - - +
2581B ASP* 3.2 24.1 + - - -
2582B ASP* 1.3 78.7 + - - +
2584B TRP* 1.4 57.7 + - - +
2586B LEU* 3.3 13.7 + - - +
2587B LEU* 2.9 29.3 + - - +
2616B ARG* 6.3 0.4 - - - -
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Residues in contact with TRP2584 (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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184A GLU* 5.7 0.7 - - - -
231A TYR* 3.5 55.2 + + + -
232A TYR* 2.7 54.1 + + + -
283A LEU* 4.7 4.5 - - - +
308B ALA* 4.9 1.2 - - + +
309B GLU 4.9 5.2 + - - -
310B ILE* 3.8 15.5 - - + -
314B ILE* 4.1 7.0 - - + -
872B TYR* 3.3 53.4 - + - -
2581B ASP* 3.0 30.2 + - - -
2582B ASP* 4.3 1.6 - - - +
2583B SER* 1.4 80.5 + - - +
2585B LEU* 1.3 94.2 + - + +
2587B LEU* 3.4 5.8 - - - +
2588B LYS* 3.2 24.7 + - - -
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Residues in contact with LEU2585 (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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310B ILE* 4.6 13.5 - - + -
311B ARG 6.1 0.7 - - - +
312B LYS 5.7 0.2 - - - +
314B ILE* 3.7 34.5 - - + -
517B GLU* 3.9 15.3 - - - +
2582B ASP* 3.0 22.4 + - + +
2584B TRP* 1.3 99.0 - - + +
2586B LEU* 1.3 66.4 + - + +
2587B LEU 3.1 1.1 - - - -
2588B LYS* 3.1 39.3 + - - +
2589B HIS* 3.2 24.0 + - + +
2618B HIS* 5.8 7.2 - - + -
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Residues in contact with LEU2586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2582B ASP* 2.8 28.0 + - + +
2583B SER* 3.3 13.2 + - - +
2585B LEU* 1.3 76.3 - - + +
2587B LEU* 1.3 61.5 + - - +
2589B HIS* 3.5 7.1 + - + +
2590B ARG* 3.1 23.8 + - - +
2612B ALA* 4.2 20.4 - - + +
2615B LEU* 3.6 37.1 - - + +
2616B ARG* 3.5 48.2 - - + +
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Residues in contact with LEU2587 (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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232A TYR* 4.1 13.9 - - + -
282A PRO 4.2 2.5 - - - +
283A LEU* 3.6 46.4 - - + +
285A ALA 3.7 21.1 - - - +
287A THR* 3.9 17.0 - - + -
2583B SER 2.9 17.7 + - - +
2584B TRP* 3.4 7.9 - - - +
2585B LEU 3.1 0.2 - - - -
2586B LEU* 1.3 77.8 - - - +
2588B LYS* 1.3 55.8 + - - +
2590B ARG* 3.2 17.5 + - - +
2591B ASP* 2.9 41.5 + - - +
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Residues in contact with LYS2588 (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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184A GLU* 4.9 10.2 + - - +
232A TYR* 3.7 21.1 - - + +
287A THR* 4.0 17.8 + - - +
288A PRO* 5.7 9.4 - - + +
289A THR* 5.8 0.2 - - + -
314B ILE* 4.1 24.0 - - - +
315B LEU 4.7 11.2 + - - -
316B ALA* 6.2 0.2 - - - +
517B GLU* 5.7 1.3 - - - -
872B TYR* 5.6 0.2 - - - -
2584B TRP* 3.2 11.1 + - + +
2585B LEU* 3.1 24.9 + - - +
2587B LEU* 1.3 77.2 - - - +
2589B HIS* 1.3 65.8 + - - +
2591B ASP* 3.3 2.8 + - - +
2592B ASN* 2.8 49.6 + - - +
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Residues in contact with HIS2589 (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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515B ASP* 2.7 46.9 + - + +
516B CYS* 3.7 16.1 - - - -
517B GLU* 2.7 39.9 + - - -
2585B LEU* 3.2 36.3 + - + +
2586B LEU* 3.9 4.3 - - + +
2587B LEU 3.3 0.2 - - - -
2588B LYS* 1.3 83.1 - - + +
2590B ARG* 1.3 60.5 + - - +
2592B ASN* 3.4 7.6 + - - +
2593B LEU* 3.3 19.3 + - - +
2611B ASP* 5.8 2.2 - - + -
2615B LEU* 3.6 33.1 - - + +
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Residues in contact with ARG2590 (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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2586B LEU 3.1 14.9 + - - +
2587B LEU* 3.5 20.9 - - - +
2589B HIS* 1.3 74.4 - - - +
2591B ASP* 1.3 66.7 + - - +
2593B LEU* 3.2 5.8 + - - +
2594B GLN* 3.1 17.5 + - + -
2605B GLU 5.2 1.4 + - - -
2608B GLN* 3.2 71.7 + - + +
2609B GLU* 4.0 19.0 + - - +
2612B ALA* 4.0 16.1 - - + +
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Residues in contact with ASP2591 (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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285A ALA 4.2 4.7 - - - +
286A PRO* 4.0 3.8 - - - +
287A THR* 3.0 47.1 + - - +
289A THR* 3.5 9.2 - - + +
2587B LEU* 2.9 27.7 + - - +
2588B LYS 3.7 0.9 - - - +
2590B ARG* 1.3 79.2 - - - +
2592B ASN* 1.4 63.2 + - - +
2594B GLN* 3.3 9.8 + - - +
2595B ASP* 3.2 28.9 + - - +
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Residues in contact with ASN2592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A THR* 3.5 27.8 - - - +
515B ASP* 2.8 38.9 + - - +
2588B LYS* 2.8 35.8 + - - +
2589B HIS* 3.7 6.4 + - - +
2590B ARG 3.3 0.4 - - - -
2591B ASP* 1.4 75.0 - - - +
2593B LEU* 1.3 61.3 + - - +
2595B ASP* 3.4 11.1 + - - +
2596B PHE* 3.3 19.0 + - + -
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Residues in contact with LEU2593 (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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506B LEU* 4.3 6.7 - - + -
514B HIS* 4.0 20.2 - - + +
515B ASP* 4.0 5.8 - - + -
2589B HIS 3.3 10.6 + - - +
2590B ARG* 3.2 9.7 + - - +
2592B ASN* 1.3 78.1 - - - +
2594B GLN* 1.3 61.0 + - - +
2596B PHE* 3.2 36.1 + - + +
2599B LEU* 3.8 28.3 - - + +
2604B LYS* 3.9 8.4 - - + +
2607B LEU* 3.8 23.8 - - + -
2608B GLN* 3.9 23.1 - - + +
2611B ASP* 3.3 25.1 - - + +
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Residues in contact with GLN2594 (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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2590B ARG* 3.1 9.2 + - + +
2591B ASP* 3.3 17.0 + - - +
2593B LEU* 1.3 74.6 - - - +
2595B ASP* 1.3 59.5 + - - +
2596B PHE 3.3 0.4 - - - -
2604B LYS* 2.7 45.4 + - - +
2608B GLN* 3.0 33.0 + - - +
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Residues in contact with ASP2595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A THR* 2.7 31.1 + - - +
290A ASP* 4.8 7.8 + - + +
2591B ASP* 3.2 17.1 + - - +
2592B ASN* 3.4 6.2 + - - +
2593B LEU 3.2 0.6 - - - -
2594B GLN* 1.3 82.0 - - - +
2596B PHE* 1.3 62.2 + - - +
2597B ILE* 3.5 3.5 + - - +
2604B LYS* 4.5 0.2 - - - -
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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