Contacts of the helix formed by residues 2600 - 2616 (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 ARG2600 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2598B ASP 5.0 3.4 - - - +
2599B LEU* 1.3 74.4 - - - +
2601B PRO* 1.4 68.8 - - + +
2602B GLU* 3.1 19.1 - - - +
2603B GLU* 2.8 44.7 + - + +
2604B LYS* 3.0 10.7 + - - +
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Residues in contact with PRO2601 (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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2599B LEU 4.3 2.9 - - - +
2600B ARG* 1.4 88.1 - - + +
2602B GLU* 1.3 65.8 + - + +
2604B LYS* 3.5 15.9 + - + +
2605B GLU* 3.1 29.3 + - - +
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Residues in contact with GLU2602 (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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2600B ARG* 3.1 25.6 - - - +
2601B PRO* 1.3 87.1 - - + +
2603B GLU* 1.4 62.9 + - + +
2605B GLU* 3.8 9.6 - - - +
2606B PHE* 3.4 19.9 + - - +
2643B LYS* 4.9 6.7 - - - +
2644B ARG* 5.5 2.7 - - - +
2645B SER* 4.1 37.6 + - - +
2646B ARG* 5.8 1.0 - - - +
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Residues in contact with GLU2603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B ALA 5.2 4.9 - - - +
502B SER* 3.0 34.2 + - - -
503B TYR* 4.4 16.7 - - + +
2598B ASP 4.4 1.9 - - - +
2599B LEU* 3.8 6.4 - - + -
2600B ARG* 2.8 42.7 + - + +
2602B GLU* 1.4 77.0 - - + +
2604B LYS* 1.4 65.2 + - - +
2606B PHE* 3.1 2.9 + - - +
2607B LEU* 2.9 42.4 + - + +
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Residues in contact with LYS2604 (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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2593B LEU* 3.9 11.4 - - - +
2594B GLN* 2.7 53.4 + - - +
2595B ASP 4.5 0.2 - - - -
2596B PHE 2.8 27.5 + - - -
2597B ILE* 5.1 0.6 - - - +
2599B LEU* 3.4 31.1 + - + +
2600B ARG 3.0 12.7 + - - +
2601B PRO* 3.6 16.8 - - + +
2603B GLU* 1.4 73.6 - - - +
2605B GLU* 1.3 55.9 - - - +
2607B LEU* 3.9 7.6 - - - +
2608B GLN* 2.9 48.6 + - - +
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Residues in contact with GLU2605 (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* 5.2 1.6 + - - -
2601B PRO 3.1 18.1 + - - +
2602B GLU* 3.8 8.9 - - - +
2603B GLU 3.2 0.2 - - - -
2604B LYS* 1.3 75.1 - - - +
2606B PHE* 1.3 62.9 + - - +
2608B GLN* 3.9 9.9 + - - +
2609B GLU* 3.3 22.5 + - - +
2639B TRP* 3.8 12.1 + - + -
2643B LYS* 4.0 17.8 + - - +
2645B SER* 4.2 9.2 + - - -
2646B ARG* 2.8 46.0 + - - +
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Residues in contact with PHE2606 (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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503B TYR* 3.4 36.8 - + - +
514B HIS* 5.7 0.9 - + - -
2602B GLU 3.4 9.1 + - - +
2603B GLU 3.1 7.0 + - - +
2605B GLU* 1.3 78.7 - - - +
2607B LEU* 1.3 56.2 + - + +
2609B GLU* 3.1 4.9 + - - +
2610B TRP* 2.9 60.3 + + + -
2632B PHE* 3.8 29.2 - + - -
2639B TRP* 4.0 13.9 - + + -
2640B LEU* 3.8 20.0 - - + -
2645B SER 5.6 1.3 - - - +
2646B ARG* 3.9 24.4 - - + +
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Residues in contact with LEU2607 (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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502B SER* 4.8 6.7 - - - -
503B TYR* 3.5 29.6 - - + +
506B LEU* 4.8 8.7 - - + -
514B HIS* 3.4 39.3 - - + +
2593B LEU* 3.8 17.3 - - + -
2599B LEU* 4.3 26.0 - - + -
2603B GLU* 2.9 39.8 + - + +
2604B LYS 4.0 1.8 - - - +
2606B PHE* 1.3 73.6 - - + +
2608B GLN* 1.4 52.8 + - - +
2610B TRP* 3.5 3.1 + - - +
2611B ASP* 2.9 40.2 + - - +
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Residues in contact with GLN2608 (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* 3.2 68.2 + - + +
2593B LEU* 3.9 16.0 - - + +
2594B GLN* 3.0 39.9 + - - +
2604B LYS* 2.9 30.9 + - - +
2605B GLU* 3.9 8.1 - - - +
2607B LEU* 1.4 71.0 - - - +
2609B GLU* 1.3 56.8 + - - +
2611B ASP* 3.8 1.8 - - - +
2612B ALA* 2.8 35.7 + - - +
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Residues in contact with GLU2609 (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* 4.0 16.2 + - - +
2605B GLU 3.3 3.9 + - - +
2606B PHE 3.1 9.0 + - - +
2608B GLN* 1.3 77.3 - - - +
2610B TRP* 1.4 65.8 + - - +
2612B ALA* 3.5 5.7 + - - +
2613B PHE* 3.4 20.1 + - - +
2632B PHE* 3.9 3.6 - - + -
2636B LYS* 2.8 42.2 + - + +
2639B TRP* 3.6 54.7 + - + +
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Residues in contact with TRP2610 (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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512B PHE* 2.7 27.0 + - + -
514B HIS* 3.8 14.6 - + - -
2606B PHE* 2.9 41.2 + + + +
2607B LEU* 3.8 3.6 - - - +
2609B GLU* 1.4 71.9 - - - +
2611B ASP* 1.4 73.8 + - - +
2613B PHE* 3.2 5.5 + - - +
2614B ILE* 2.8 67.9 + - + +
2625B LEU* 4.2 19.3 - - + -
2629B PHE* 4.4 25.1 - + - -
2632B PHE* 3.7 57.7 - + + -
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Residues in contact with ASP2611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513B SER* 3.1 19.7 + - - +
514B HIS* 2.9 40.2 + - - -
515B ASP* 3.2 12.8 + - - +
2589B HIS* 5.8 1.8 - - + -
2593B LEU* 3.3 19.5 - - + +
2607B LEU 2.9 24.7 + - - +
2608B GLN* 4.1 4.3 - - - +
2610B TRP* 1.4 74.5 - - - +
2612B ALA* 1.3 65.8 + - - +
2614B ILE* 4.2 4.5 - - - -
2615B LEU* 2.8 39.5 + - + +
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Residues in contact with ALA2612 (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* 4.2 21.0 - - + +
2590B ARG* 4.0 17.5 - - + +
2608B GLN 2.8 23.1 + - - +
2609B GLU* 3.8 7.2 - - - +
2610B TRP 3.4 0.2 - - - -
2611B ASP* 1.3 73.7 - - - +
2613B PHE* 1.3 59.9 + - - +
2615B LEU* 5.1 0.9 - - - -
2616B ARG* 3.3 28.4 + - - +
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Residues in contact with PHE2613 (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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2609B GLU 3.4 9.5 + - - +
2610B TRP* 3.2 8.7 + + - +
2611B ASP 3.1 0.2 - - - -
2612B ALA* 1.3 77.6 - - - +
2614B ILE* 1.3 78.1 + - + +
2616B ARG* 3.5 8.1 - - - +
2617B ARG* 3.0 62.0 + - + +
2628B TYR* 3.2 27.1 - - + -
2631B ARG* 3.8 8.5 - - + -
2632B PHE* 3.5 45.1 - + + -
2635B GLU* 3.5 26.9 - - - -
2636B LYS* 4.5 12.3 - - - -
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Residues in contact with ILE2614 (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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511B CYS* 3.8 9.8 - - - +
512B PHE* 4.4 2.2 - - + -
513B SER* 3.6 37.5 - - - +
2610B TRP* 2.8 59.0 + - + +
2611B ASP* 4.2 1.8 - - - -
2613B PHE* 1.3 82.6 - - + +
2615B LEU* 1.4 67.7 + - - +
2617B ARG* 3.1 20.5 + - + +
2618B HIS 3.9 2.4 + - - -
2619B ILE* 3.7 31.7 + - + +
2625B LEU* 4.5 3.4 - - + -
2628B TYR* 3.8 20.9 - - + -
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Residues in contact with LEU2615 (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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511B CYS* 5.0 4.0 - - - -
513B SER* 3.5 25.4 - - - +
515B ASP 3.6 12.6 - - - +
516B CYS* 4.0 14.4 - - + -
517B GLU* 5.1 4.5 - - + +
2586B LEU* 3.6 22.7 - - + +
2589B HIS* 3.6 41.3 - - + +
2611B ASP* 2.8 32.4 + - + +
2612B ALA* 4.8 0.9 - - - +
2614B ILE* 1.4 72.7 - - - +
2616B ARG* 1.3 60.5 + - - +
2617B ARG 3.2 1.2 + - - -
2618B HIS* 3.2 26.6 + - - -
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Residues in contact with ARG2616 (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 ASP* 4.2 17.3 - - - +
2583B SER* 6.3 0.2 - - - -
2586B LEU* 3.5 31.4 - - + +
2612B ALA* 3.3 22.1 + - - +
2613B PHE* 3.5 10.1 - - - +
2615B LEU* 1.3 76.1 - - - +
2617B ARG* 1.4 74.1 + - - +
2618B HIS* 3.2 21.3 + - - -
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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
------------------------------------------------------------
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