Contacts of the helix formed by residues 709 - 717 (chain A) in PDB entry 2KFN
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 ILE 709 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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706A TYR* 3.6 25.4 + - + -
707A SER 3.1 4.9 + - - -
708A GLN* 1.3 74.8 - - - +
710A GLU* 1.3 80.1 + - - +
712A ARG* 3.1 7.8 + - - +
713A ILE* 2.9 40.5 + - + +
852A ALA* 4.0 17.3 - - + +
855A ILE* 3.8 40.2 - - + -
856A ILE* 5.0 1.1 - - + -
882A ASP* 3.5 22.2 + - + +
914A LEU* 3.8 20.6 - - + -
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Residues in contact with GLU 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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320A ZN 2.3 35.3 - - - -
668A ARG* 2.9 19.6 + - - +
708A GLN* 4.0 6.8 - - - +
709A ILE* 1.3 84.2 + - + +
711A LEU* 1.3 57.2 + - - +
713A ILE* 3.4 11.5 + - - +
714A MET* 2.9 27.9 + - - +
762A PHE* 5.3 6.8 - - - -
765A ILE* 3.9 28.6 - - + +
848A MET* 4.2 15.2 - - + +
849A GLN* 5.1 3.6 - - + -
852A ALA* 4.4 4.9 - - + -
882A ASP* 2.8 7.4 - - - +
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Residues in contact with LEU 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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708A GLN* 3.3 17.1 + - + +
709A ILE 3.2 0.6 - - - -
710A GLU* 1.3 76.8 + - - +
712A ARG* 1.3 61.0 + - - +
714A MET* 3.4 18.7 + - + +
715A ALA* 3.0 26.3 + - - +
723A LEU* 5.6 0.2 - - - +
727A PHE* 3.8 14.3 - - + -
733A ILE* 3.7 29.4 - - + -
734A HIS* 3.7 9.0 - - - +
761A ASN* 3.8 28.0 - - + +
762A PHE* 3.5 24.5 - - + -
765A ILE* 3.4 26.9 - - + +
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Residues in contact with ARG 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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707A SER* 3.1 25.2 + - - -
708A GLN* 3.2 12.0 + - - +
709A ILE* 3.1 11.1 + - + +
711A LEU* 1.3 74.1 - - - +
713A ILE* 1.3 64.3 + - - +
715A ALA* 3.3 4.2 + - - +
716A HIS* 3.1 21.7 + - - +
727A PHE* 3.6 61.2 + - + +
912A VAL* 3.9 12.0 - - + +
913A PRO* 2.8 51.1 + - + +
914A LEU* 4.3 8.2 + - - +
915A LEU* 3.4 41.1 - - - +
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Residues in contact with ILE 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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709A ILE* 2.9 29.9 + - + +
710A GLU* 3.5 5.4 - - - +
711A LEU 3.2 0.2 - - - -
712A ARG* 1.3 74.9 - - - +
714A MET* 1.3 59.9 + - - +
716A HIS* 3.2 4.8 + - - +
717A LEU* 2.9 39.0 + - + +
818A LEU* 5.3 1.3 - - + -
848A MET* 3.5 32.3 - - + +
851A THR* 3.8 21.8 - - + -
852A ALA* 3.5 37.5 - - + +
855A ILE* 4.1 2.5 - - + -
912A VAL* 3.9 22.2 - - + -
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Residues in contact with MET 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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321A MG 4.1 3.6 - - - -
710A GLU 2.9 13.7 + - - +
711A LEU* 3.7 21.1 - - + +
713A ILE* 1.3 76.5 - - - +
715A ALA* 1.3 54.6 + - - +
717A LEU* 3.9 3.0 - - - +
718A SER* 2.8 38.0 + - - +
723A LEU* 4.0 18.8 - - + -
761A ASN* 4.7 1.8 - - - +
764A LEU* 4.1 26.9 - - + -
765A ILE* 4.4 9.6 - - + -
791A TYR* 3.8 21.8 - - - +
798A VAL* 4.4 15.3 - - + -
801A TYR* 5.3 7.9 - - + -
848A MET* 3.3 32.1 - - + +
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Residues in contact with ALA 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 LEU 3.0 13.2 + - - +
712A ARG 3.4 10.5 - - - +
713A ILE 3.2 0.2 - - - -
714A MET* 1.3 76.5 - - - +
716A HIS* 1.3 60.3 + - - +
718A SER* 3.3 7.0 + - - -
719A ARG 3.2 15.9 + - - -
720A ASP 3.5 1.9 + - - -
723A LEU* 3.8 26.2 - - + +
724A LEU* 3.0 30.7 - - + +
727A PHE* 4.0 15.0 - - + -
913A PRO* 5.4 0.9 - - + -
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Residues in contact with HIS 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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712A ARG 3.1 9.6 + - - +
713A ILE 3.2 7.8 + - - +
715A ALA* 1.3 78.8 - - - +
717A LEU* 1.3 76.7 + - + +
719A ARG* 3.1 22.4 + - - +
724A LEU* 3.8 8.9 - - - +
818A LEU* 4.0 20.6 - - + +
911A ASP* 3.5 47.4 + - + -
912A VAL* 4.3 11.0 - - + -
913A PRO* 4.6 7.6 - - + +
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Residues in contact with LEU 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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713A ILE* 2.9 28.5 + - + +
714A MET* 4.0 4.5 - - - +
716A HIS* 1.3 79.8 - - + +
718A SER* 1.3 57.4 + - - +
719A ARG* 3.6 8.2 + - - +
801A TYR* 3.6 35.7 - - + +
804A ARG* 2.8 26.7 + - - -
818A LEU* 3.3 29.2 - - + -
847A PRO* 4.1 15.3 - - + +
848A MET* 3.8 25.4 - - + -
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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