Contacts of the helix formed by residues 2624 - 2643 (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 TYR2624 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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757B PRO* 3.4 31.4 - - + +
766B ARG* 2.6 30.6 + - + -
769B ALA* 3.4 15.0 - - - +
770B ASP* 3.3 41.0 + - + -
771B PRO* 5.0 6.1 - - + -
790B GLN* 5.5 0.9 - - - -
2619B ILE* 5.1 5.8 - - + -
2620B SER 6.0 0.7 - - - -
2621B SER* 3.3 22.3 + - - +
2622B GLU 3.2 0.6 - - - -
2623B GLN* 1.4 88.2 - - + +
2625B LEU* 1.4 65.4 + - - +
2626B PRO* 3.5 2.0 - - - -
2627B ARG* 3.5 19.6 + - - +
2628B TYR* 3.1 44.5 + + + -
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Residues in contact with LEU2625 (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* 3.6 61.0 - - + -
2610B TRP* 4.2 22.0 - - + -
2614B ILE* 4.5 8.7 - - + -
2619B ILE* 4.7 6.9 - - + +
2621B SER 4.0 2.8 + - - -
2622B GLU* 3.0 17.6 + - + +
2624B TYR* 1.4 76.2 - - - +
2626B PRO* 1.4 59.9 - - + +
2628B TYR* 3.1 3.2 + - - +
2629B PHE* 2.8 33.9 + - + +
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Residues in contact with PRO2626 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2622B GLU 3.4 12.8 - - - +
2623B GLN* 3.7 10.3 - - - +
2624B TYR 3.6 3.1 - - - -
2625B LEU* 1.4 91.3 - - + +
2627B ARG* 1.3 56.1 + - - +
2629B PHE* 3.6 8.5 - - + +
2630B LEU* 3.0 38.2 + - + +
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Residues in contact with ARG2627 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770B ASP* 2.7 43.2 + - - -
772B GLU* 3.3 24.5 + - - +
2623B GLN 5.9 0.4 - - - +
2624B TYR* 3.5 23.9 + - - +
2625B LEU 3.3 0.6 - - - -
2626B PRO* 1.3 78.7 - - - +
2628B TYR* 1.3 80.8 + - - +
2630B LEU* 3.6 7.8 + - - +
2631B ARG* 3.2 59.2 + - - +
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Residues in contact with TYR2628 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770B ASP* 4.7 0.2 + - - -
771B PRO* 4.6 13.1 - - + +
772B GLU* 2.9 29.9 + - - +
2613B PHE* 3.2 14.7 - + + -
2614B ILE* 3.8 21.3 - - + -
2617B ARG* 3.7 38.6 + - + +
2619B ILE* 3.5 27.1 - - + -
2624B TYR* 3.1 36.9 + + + -
2625B LEU 3.1 5.8 + - - +
2627B ARG* 1.3 90.6 + - - +
2629B PHE* 1.3 60.0 + - - +
2631B ARG* 3.4 20.0 + - - -
2632B PHE* 2.9 24.3 + - - +
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Residues in contact with PHE2629 (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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616B PHE* 5.7 10.5 - + - -
2610B TRP* 4.4 28.4 - + + -
2625B LEU* 2.8 25.3 + - + +
2626B PRO* 3.6 9.6 - - + +
2628B TYR* 1.3 74.4 - - - +
2630B LEU* 1.4 69.3 + - + +
2632B PHE* 3.0 10.4 + + - +
2633B VAL* 2.9 54.6 + - + +
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Residues in contact with LEU2630 (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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2626B PRO* 3.0 22.2 + - + +
2627B ARG* 3.8 6.7 - - - +
2628B TYR 3.4 0.2 - - - -
2629B PHE* 1.4 88.0 - - + +
2631B ARG* 1.3 55.8 + - - +
2633B VAL* 3.2 10.3 + - + +
2634B ARG* 2.8 66.4 + - + +
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Residues in contact with ARG2631 (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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772B GLU* 3.1 39.6 + - - -
2613B PHE* 3.8 12.8 - - + -
2617B ARG* 5.0 9.8 - - - +
2627B ARG* 3.2 40.8 + - - +
2628B TYR* 3.7 20.9 - - - +
2630B LEU* 1.3 75.9 - - - +
2632B PHE* 1.4 56.1 + - - +
2634B ARG* 3.5 20.9 + - - +
2635B GLU* 2.9 43.8 + - - +
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Residues in contact with PHE2632 (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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2606B PHE* 3.8 30.5 - + - -
2609B GLU* 3.9 12.1 - - + -
2610B TRP* 3.7 52.9 - + + -
2613B PHE* 3.5 35.1 - + + -
2628B TYR 2.9 14.5 + - - +
2629B PHE* 3.0 10.5 + + - +
2631B ARG* 1.4 74.5 - - - +
2633B VAL* 1.3 62.1 + - + +
2635B GLU* 3.2 1.7 + - - +
2636B LYS* 2.8 64.5 + - + +
2640B LEU* 3.9 17.7 - - + -
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Residues in contact with VAL2633 (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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2629B PHE* 2.9 54.0 + - + +
2630B LEU* 3.6 13.0 - - + +
2632B PHE* 1.3 79.9 - - + +
2634B ARG* 1.4 58.7 + - + +
2636B LYS 3.8 0.2 - - - -
2637B ALA* 3.0 32.4 + - + +
2640B LEU* 4.9 12.9 - - + +
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Residues in contact with ARG2634 (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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2627B ARG 5.6 0.2 + - - -
2630B LEU* 2.8 55.9 + - + +
2631B ARG* 3.8 34.9 - - - +
2633B VAL* 1.4 73.5 - - + +
2635B GLU* 1.3 61.7 + - + +
2637B ALA* 3.7 13.4 - - - +
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Residues in contact with GLU2635 (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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2613B PHE* 3.5 27.9 - - - -
2617B ARG* 4.3 7.7 + - - -
2631B ARG* 2.9 24.9 + - - +
2632B PHE* 3.9 2.5 - - - +
2634B ARG* 1.3 79.0 - - + +
2636B LYS* 1.3 74.7 + - + +
2637B ALA 3.3 2.0 + - - -
2638B ASP* 4.9 2.9 + - - +
2639B TRP* 5.6 0.5 + - - +
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Residues in contact with LYS2636 (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* 2.8 38.6 + - + +
2613B PHE* 4.5 17.0 - - + -
2632B PHE* 2.8 52.6 + - + +
2633B VAL 3.8 1.3 - - - -
2635B GLU* 1.3 86.1 + - + +
2637B ALA* 1.3 54.9 + - - +
2638B ASP 3.3 2.5 - - - -
2639B TRP* 3.1 17.0 + - + +
2640B LEU* 2.8 50.3 + - + +
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Residues in contact with ALA2637 (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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2633B VAL* 3.0 19.9 + - + +
2634B ARG* 3.7 13.7 - - - +
2635B GLU 3.3 1.4 - - - +
2636B LYS* 1.3 76.6 - - - +
2638B ASP* 1.4 67.2 + - - +
2640B LEU* 3.6 5.1 + - - +
2641B VAL* 3.2 30.1 + - - +
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Residues in contact with ASP2638 (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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2635B GLU 4.9 2.5 + - - +
2636B LYS 3.3 0.8 - - - -
2637B ALA* 1.4 80.9 - - - +
2639B TRP* 1.3 62.1 + - - +
2641B VAL* 3.5 10.6 + - - +
2642B SER* 2.8 35.7 + - - +
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Residues in contact with TRP2639 (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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2605B GLU* 3.8 24.2 + - + -
2606B PHE* 4.0 15.7 - + - -
2609B GLU* 3.6 53.4 + - + +
2632B PHE* 5.1 0.7 - + - -
2635B GLU 5.6 0.4 + - - -
2636B LYS* 3.1 18.9 + - + +
2638B ASP* 1.3 76.4 - - - +
2640B LEU* 1.4 90.0 + - + +
2642B SER* 3.5 7.0 + - - -
2646B ARG* 2.9 81.3 + - + +
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Residues in contact with LEU2640 (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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2606B PHE* 3.8 20.2 - - + -
2632B PHE* 3.9 22.2 - - + -
2633B VAL* 4.9 14.1 - - + -
2636B LYS* 2.8 30.0 + - + +
2637B ALA* 3.8 6.3 - - - +
2639B TRP* 1.4 97.0 - - + +
2641B VAL* 1.3 61.5 + - + +
2643B LYS 3.2 22.5 - - - +
2646B ARG* 3.8 17.8 - - - +
2647B GLY* 3.7 16.9 + - - +
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Residues in contact with VAL2641 (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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619B ALA 4.8 13.5 - - - +
2637B ALA 3.2 18.3 + - - +
2638B ASP* 3.6 16.4 - - - +
2640B LEU* 1.3 77.1 - - + +
2642B SER* 1.3 63.0 + - - +
2643B LYS* 3.4 3.5 + - - -
2644B ARG 5.1 0.2 + - - -
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Residues in contact with SER2642 (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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2638B ASP* 2.8 23.7 + - - +
2639B TRP* 3.6 9.0 - - - -
2640B LEU 3.3 1.2 - - - -
2641B VAL* 1.3 77.6 - - - +
2643B LYS* 1.3 57.8 + - - +
2646B ARG* 4.0 8.5 - - - -
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Residues in contact with LYS2643 (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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2602B GLU* 4.9 7.7 - - - +
2605B GLU* 4.0 12.0 + - - +
2639B TRP 4.0 1.6 + - - -
2640B LEU 3.2 18.2 + - - +
2641B VAL 4.6 2.7 - - - -
2642B SER* 1.3 78.7 - - - +
2644B ARG* 1.3 73.6 + - - +
2645B SER* 3.0 32.3 + - - +
2646B ARG* 3.3 43.4 + - + +
2647B GLY 3.7 0.9 + - - -
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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
------------------------------------------------------------
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