Contacts of the helix formed by residues 705 - 719 (chain B) in PDB entry 4KSP
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 LEU 705 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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567B HIS* 5.7 1.3 - - - +
634B PHE* 4.1 28.3 - - + -
635B GLN* 4.1 33.2 - - + +
638B VAL* 4.5 3.1 - - + -
703B ARG 5.2 1.3 - - - +
704B PRO* 1.3 77.7 - - - +
706B PHE* 1.3 67.0 + - - +
707B PRO* 3.6 6.7 - - + -
708B GLN* 3.5 24.1 + - - +
709B ILE* 3.3 20.8 + - - +
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Residues in contact with PHE 706 (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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560B ALA* 3.9 23.8 - - + -
563B MET* 3.5 37.2 - - + -
564B ASP* 3.9 18.4 - - + +
567B HIS* 3.6 35.8 + + + +
637B ASP 4.4 0.2 - - - -
638B VAL* 3.5 29.4 - - + -
641B PHE* 3.8 39.7 - + + -
705B LEU* 1.3 69.0 - - - +
707B PRO* 1.3 77.4 - - + +
708B GLN 3.1 1.8 - - - -
709B ILE* 2.9 14.5 + - + +
710B LEU* 2.8 25.8 + - - +
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Residues in contact with PRO 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564B ASP* 3.4 26.2 - - - +
567B HIS* 6.5 0.2 - - + -
705B LEU* 3.8 10.8 - - + -
706B PHE* 1.3 88.8 - - + +
708B GLN* 1.3 67.9 + - - +
710B LEU* 3.7 7.3 - - + +
711B ALA* 2.9 30.5 + - - +
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Residues in contact with GLN 708 (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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691B LEU* 5.7 0.2 - - - -
704B PRO* 4.3 15.7 - - + -
705B LEU* 3.6 36.8 - - - +
706B PHE 3.1 0.4 - - - -
707B PRO* 1.3 84.2 - - - +
709B ILE* 1.3 61.0 + - - +
711B ALA* 3.4 6.6 + - - +
712B SER* 2.9 33.1 + - - -
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Residues in contact with ILE 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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560B ALA* 4.2 7.2 - - + -
638B VAL* 3.9 19.3 - - + -
641B PHE* 3.7 19.7 - - + -
691B LEU* 4.1 24.7 - - + -
695B CYS* 3.8 18.4 - - - -
704B PRO* 4.2 10.8 - - + +
705B LEU 3.3 17.5 + - - +
706B PHE* 2.9 26.3 + - + +
708B GLN* 1.3 74.3 - - - +
710B LEU* 1.3 66.4 + - - +
712B SER* 3.1 1.9 + - - -
713B ILE* 2.9 45.1 + - + +
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Residues in contact with LEU 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A HIS* 5.3 2.5 - - - -
477A GLY 5.2 4.9 - - - +
557B ARG* 3.8 14.6 - - + +
560B ALA* 3.7 25.3 - - + +
561B GLN* 3.8 34.5 - - + +
564B ASP* 3.8 28.5 - - + +
706B PHE 2.8 18.1 + - - +
707B PRO* 3.7 5.8 - - + +
709B ILE* 1.3 73.7 - - - +
711B ALA* 1.3 57.4 + - - +
713B ILE* 3.8 3.7 - - + +
714B GLU* 2.9 53.2 + - - +
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Residues in contact with ALA 711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707B PRO 2.9 19.0 + - - +
708B GLN* 3.6 8.7 - - - +
710B LEU* 1.3 77.2 - - - +
712B SER* 1.3 60.7 + - - +
714B GLU* 3.6 11.3 + - - +
715B LEU* 3.1 22.7 + - - +
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Residues in contact with SER 712 (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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687B ALA* 5.7 0.7 - - - +
691B LEU* 4.3 23.9 - - - +
708B GLN* 2.9 18.6 + - - +
709B ILE 3.7 4.0 - - - -
711B ALA* 1.3 76.2 - - - +
713B ILE* 1.3 62.2 + - - +
715B LEU* 3.4 12.5 - - - +
716B LEU* 3.4 25.8 + - - +
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Residues in contact with ILE 713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B ILE* 4.3 18.8 - - + +
556B ALA* 4.3 11.4 - - + +
557B ARG* 3.9 31.4 - - + +
560B ALA* 4.1 16.6 - - + -
641B PHE* 4.2 9.4 - - + -
645B LEU* 5.5 0.7 - - + -
688B MET* 4.5 9.6 - - + -
691B LEU* 3.6 20.9 - - + -
709B ILE* 2.9 38.8 + - + +
710B LEU* 3.8 4.5 - - + +
712B SER* 1.3 74.1 - - - +
714B GLU* 1.3 60.2 + - - +
716B LEU* 3.4 8.5 + - - +
717B ALA* 2.8 32.5 + - + +
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Residues in contact with GLU 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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474A LYS* 3.6 25.3 + - - +
477A GLY 5.7 0.3 + - - -
557B ARG* 4.3 19.3 - - + +
561B GLN* 3.8 9.5 + - - -
710B LEU* 2.9 42.9 + - + +
711B ALA* 3.9 11.0 - - - +
713B ILE* 1.3 76.2 - - - +
715B LEU* 1.3 61.4 + - - +
717B ALA* 3.7 7.4 - - - +
718B ARG* 3.0 42.7 + - - +
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Residues in contact with LEU 715 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687B ALA* 6.3 2.5 - - + -
711B ALA 3.1 14.1 + - - +
712B SER* 3.4 14.6 - - - +
713B ILE 3.1 0.8 - - - -
714B GLU* 1.3 79.0 - - - +
716B LEU* 1.3 64.1 + - + +
718B ARG* 3.6 28.5 + - - +
719B SER* 3.5 9.7 + - - -
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Residues in contact with LEU 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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553B ILE* 4.0 31.0 - - + -
685B PRO* 4.6 13.9 - - + -
687B ALA* 3.6 34.5 - - + -
688B MET* 3.7 33.2 - - + +
691B LEU* 5.8 1.8 - - + -
712B SER 3.4 11.8 + - - +
713B ILE* 3.4 9.6 + - + +
715B LEU* 1.3 79.3 - - + +
717B ALA* 1.3 72.7 + - - +
719B SER* 3.0 28.2 + - - +
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Residues in contact with ALA 717 (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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553B ILE* 4.7 15.0 - - + -
557B ARG* 5.1 9.6 - - - +
713B ILE* 2.8 21.8 + - + +
714B GLU* 3.7 10.8 - - - +
715B LEU 3.3 0.2 - - - -
716B LEU* 1.3 86.3 - - - +
718B ARG* 1.3 64.6 + - - +
719B SER 3.2 5.7 + - - +
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Residues in contact with ARG 718 (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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714B GLU* 3.0 41.2 + - - +
715B LEU* 3.6 18.5 + - - +
716B LEU 3.4 0.4 - - - -
717B ALA* 1.3 81.7 - - - +
719B SER* 1.3 65.7 + - - +
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Residues in contact with SER 719 (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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715B LEU 3.5 5.1 + - - -
716B LEU* 3.0 39.7 + - - +
717B ALA 3.3 6.2 - - - +
718B ARG* 1.3 85.6 - - - +
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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