Contacts of the helix formed by residues 705 - 716 (chain B) in PDB entry 3KXX
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 PRO 705 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665B LYS* 5.2 0.7 - - - +
703B GLY 3.4 9.6 - - - +
704B VAL* 1.3 85.0 - - + +
706B VAL* 1.3 68.0 + - - +
707B GLU* 3.2 18.2 - - - +
708B GLU* 2.9 38.5 + - + +
709B LEU* 3.1 10.0 + - - +
517C LYS 6.1 0.2 - - - +
518C SER* 6.4 1.1 - - - -
556C PRO* 3.7 34.8 - - + -
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Residues in contact with VAL 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664B VAL* 3.2 40.2 - - + -
665B LYS* 4.8 4.4 - - - +
704B VAL 3.8 1.6 + - - -
705B PRO* 1.3 69.5 - - - +
707B GLU* 1.3 70.8 + - - +
709B LEU* 3.0 21.2 + - - +
710B PHE* 3.5 28.8 + - + -
516C LEU* 4.9 5.8 - - + -
517C LYS 4.0 12.0 + - - +
518C SER* 4.2 10.7 - - - +
520C ALA* 3.9 26.2 - - + +
521C THR 5.7 1.1 - - - +
522C GLU* 6.3 0.2 - - - -
525C LEU* 4.6 8.1 - - + -
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Residues in contact with GLU 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705B PRO* 3.2 25.3 - - - +
706B VAL* 1.3 74.5 - - - +
708B GLU* 1.3 62.0 + - - +
709B LEU 3.4 0.3 + - - -
710B PHE* 3.4 27.9 + - + +
711B LYS* 4.3 2.9 + - - +
465C LEU* 6.1 5.6 - - + -
516C LEU* 3.2 27.2 + - - +
525C LEU* 3.8 24.2 - - + -
555C GLY 4.4 9.0 - - - +
556C PRO* 3.3 6.6 - - - +
557C LEU* 3.1 33.3 + - + +
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Residues in contact with GLU 708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704B VAL* 4.1 8.3 - - + -
705B PRO* 2.9 30.3 + - + +
707B GLU* 1.3 80.3 + - - +
709B LEU* 1.3 62.4 + - - +
711B LYS* 3.5 16.8 + - - +
712B LEU* 3.4 25.5 + - + +
554C ASP* 5.8 0.5 - - - +
555C GLY* 3.1 36.2 + - - -
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Residues in contact with LEU 709 (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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664B VAL* 4.5 9.0 - - + +
665B LYS* 4.2 24.9 - - + -
672B LEU* 6.4 0.2 - - + -
701B TYR* 3.6 50.9 - - + -
704B VAL* 3.9 13.2 - - + +
705B PRO 3.1 8.9 + - - +
706B VAL* 3.0 11.9 + - - +
708B GLU* 1.3 76.0 - - - +
710B PHE* 1.3 68.8 + - + +
712B LEU* 2.9 14.3 + - + -
713B LEU* 2.8 50.7 + - + +
717B HIS* 4.8 1.8 - - - +
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Residues in contact with PHE 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664B VAL* 4.4 10.5 - - + -
672B LEU* 4.0 38.1 - - + -
673B PHE* 3.3 34.1 - + + -
706B VAL* 3.5 28.9 - - + -
707B GLU* 3.4 21.5 - - - +
709B LEU* 1.3 78.6 - - + +
711B LYS* 1.3 61.2 + - - +
713B LEU* 3.8 4.0 + - + -
714B LYS* 3.5 10.3 - - - +
461C SER* 3.6 20.4 - - - -
462C GLU* 4.4 21.3 - - + +
522C GLU* 5.2 3.4 - - + -
525C LEU* 3.4 31.9 - - + -
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Residues in contact with LYS 711 (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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707B GLU 4.3 2.0 + - - +
708B GLU* 3.5 17.3 + - - +
709B LEU 3.1 0.8 - - - -
710B PHE* 1.3 77.3 - - - +
712B LEU* 1.3 73.9 + - + +
714B LYS* 3.1 19.7 + - + +
715B GLU* 2.7 48.0 + - - +
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Residues in contact with LEU 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704B VAL* 3.6 35.4 - - + -
708B GLU* 3.4 17.7 + - + +
709B LEU* 2.9 11.7 + - + +
711B LYS* 1.3 84.9 - - + +
713B LEU* 1.3 62.5 + - - +
715B GLU* 3.0 22.0 + - + +
716B GLY 3.1 0.2 + - - -
717B HIS* 2.9 61.0 + - + +
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Residues in contact with LEU 713 (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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664B VAL 5.4 2.2 - - - +
667B MET 5.5 4.0 - - - +
669B PRO* 5.5 9.5 - - + +
672B LEU* 3.8 28.9 - - + -
673B PHE* 4.1 16.2 - - + -
684B TRP* 4.6 14.8 - - + -
701B TYR* 4.2 17.0 - - + +
709B LEU* 2.8 52.2 + - + +
710B PHE* 3.9 5.4 - - - +
712B LEU* 1.3 71.8 - - - +
714B LYS* 1.3 61.4 + - - +
716B GLY* 3.2 13.0 + - - -
717B HIS 4.1 15.9 + - - +
718B ARG* 4.2 9.2 + - - +
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Residues in contact with LYS 714 (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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673B PHE* 3.4 35.3 - - + +
710B PHE* 3.5 14.8 - - - +
711B LYS* 3.1 11.8 + - + +
713B LEU* 1.3 72.2 - - - +
715B GLU* 1.3 69.8 + - - +
716B GLY* 3.0 3.6 + - - -
462C GLU 5.4 0.7 - - - -
463C TYR* 2.7 47.6 + - + -
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Residues in contact with GLU 715 (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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711B LYS* 2.7 51.2 + - - +
712B LEU* 3.0 25.7 + - + +
714B LYS* 1.3 80.8 - - - +
716B GLY* 1.3 56.2 + - - +
717B HIS* 4.3 3.8 - - + +
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Residues in contact with GLY 716 (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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712B LEU 3.1 0.8 + - - -
713B LEU 3.2 8.0 + - - -
714B LYS 3.0 5.5 - - - -
715B GLU* 1.3 80.3 - - - +
717B HIS* 1.3 69.6 + - - +
718B ARG* 3.6 18.3 + - - +
734B ARG* 5.3 1.9 + - - -
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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
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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