Contacts of the helix formed by residues 708 - 718 (chain A) in PDB entry 3KAS
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 THR 708 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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699A HIS 3.8 5.2 - - - +
700A VAL* 3.4 13.5 - - - +
701A PHE 5.3 0.9 - - - -
703A GLY 3.5 34.2 + - - +
704A SER* 4.0 0.2 - - - -
705A GLY 3.4 20.8 + - - +
706A SER 3.4 1.6 - - - +
707A HIS* 1.3 93.8 - - + +
709A LEU* 1.3 64.2 + - - +
710A PRO* 3.5 12.1 - - - +
711A ALA* 2.9 24.9 + - - +
712A LEU* 3.2 9.9 + - - +
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Residues in contact with LEU 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618A LEU* 4.7 4.3 - - + -
621A PHE* 3.5 53.6 - - + -
700A VAL* 2.8 26.5 + - + +
701A PHE* 3.8 39.3 - - + -
707A HIS 3.9 1.5 + - - +
708A THR* 1.3 70.2 - - - +
710A PRO* 1.3 70.5 - - + +
712A LEU* 3.0 18.1 + - + +
713A LEU* 3.1 14.9 + - - +
738A ALA* 3.8 26.2 - - + -
742A ILE* 4.8 6.3 - - + -
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Residues in contact with PRO 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534A LYS* 4.7 15.0 - - - +
700A VAL 3.6 7.6 - - - +
701A PHE* 4.2 15.9 - - + +
708A THR* 3.5 12.1 - - - +
709A LEU* 1.3 94.1 - - + +
711A ALA* 1.3 61.2 + - - +
713A LEU* 3.1 13.4 + - + +
714A GLU* 2.9 35.0 + - + +
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Residues in contact with ALA 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705A GLY 3.1 28.0 - - - +
706A SER* 3.7 16.6 - - - -
708A THR* 2.9 12.0 + - - +
710A PRO* 1.3 78.4 - - - +
712A LEU* 1.3 62.8 + - - +
714A GLU* 3.2 12.0 + - - +
715A ASN* 3.0 26.3 + - - +
734A GLN* 3.8 4.5 + - - +
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Residues in contact with LEU 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621A PHE* 4.3 16.8 - - + -
625A LEU* 3.9 29.6 - - + -
706A SER 5.7 0.2 - - - +
708A THR 3.2 5.1 + - - +
709A LEU* 3.0 14.6 + - + +
711A ALA* 1.3 78.5 - - - +
713A LEU* 1.3 67.2 + - + +
715A ASN* 3.6 3.1 + - - +
716A LEU* 3.4 18.6 + - + +
731A PHE* 4.0 17.1 - - + -
734A GLN* 3.6 52.6 - - + +
735A LEU* 3.7 14.6 - - + +
738A ALA* 4.4 11.9 - - + -
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Residues in contact with LEU 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621A PHE* 4.0 21.3 - - + -
624A ASP* 3.9 29.4 - - + +
625A LEU* 4.1 38.1 - - + +
628A TYR* 4.4 17.1 + - + +
709A LEU 3.1 9.2 + - - +
710A PRO* 3.1 13.6 + - + +
712A LEU* 1.3 76.6 - - + +
714A GLU* 1.3 59.8 + - + +
716A LEU* 3.0 5.4 + - + +
717A LYS* 2.8 30.4 + - - +
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Residues in contact with GLU 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A LYS* 6.0 0.5 + - - -
710A PRO* 2.9 27.3 + - - +
711A ALA* 3.8 10.1 - - - +
713A LEU* 1.3 77.0 - - + +
715A ASN* 1.3 62.5 + - - +
716A LEU 3.3 0.5 + - - -
717A LYS* 3.4 19.7 + - + +
718A LEU* 3.3 28.5 + - + +
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Residues in contact with ASN 715 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711A ALA 3.0 16.6 + - - +
712A LEU 3.8 1.8 - - - +
713A LEU 3.2 0.2 - - - -
714A GLU* 1.3 76.5 - - - +
716A LEU* 1.3 59.0 + - - +
718A LEU* 3.6 14.8 - - - +
725A ALA 4.3 3.5 - - - +
726A PHE* 2.8 30.1 - - - -
727A ASN* 3.4 41.4 + - - +
730A LEU* 3.9 13.9 - - + +
731A PHE* 3.5 16.6 - - - +
734A GLN* 3.3 25.4 + - - +
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Residues in contact with LEU 716 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625A LEU* 3.4 33.0 - - + -
628A TYR* 3.7 41.3 - - + -
631A ASP* 5.2 2.0 - - + -
632A ILE* 4.5 6.5 - - + -
635A MET* 5.1 2.9 - - - -
712A LEU* 3.4 12.1 + - + +
713A LEU* 3.0 10.4 + - + +
715A ASN* 1.3 78.5 - - - +
717A LYS* 1.3 62.7 + - - +
718A LEU 3.0 1.8 - - - -
719A ARG* 3.2 27.7 + - - +
720A LYS 4.6 0.3 + - - -
726A PHE* 4.1 15.5 - - + -
731A PHE* 3.6 35.0 - - + -
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Residues in contact with LYS 717 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628A TYR* 3.6 23.0 + - - +
713A LEU 2.8 15.0 + - - +
714A GLU* 3.4 18.8 + - + +
716A LEU* 1.3 71.7 - - - +
718A LEU* 1.3 62.6 + - + +
719A ARG 3.0 9.7 + - - -
720A LYS* 3.6 26.4 + - + +
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Residues in contact with LEU 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714A GLU* 3.3 16.4 + - + +
715A ASN* 3.6 17.0 - - - +
716A LEU 3.0 0.8 - - - -
717A LYS* 1.3 83.3 - - + +
719A ARG* 1.3 56.1 + - - -
720A LYS 3.5 0.9 - - - -
721A GLN* 3.5 40.5 - - + +
723A ASN 4.5 0.2 - - - +
725A ALA* 3.8 26.0 - - + +
726A PHE* 3.0 24.7 + - - +
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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