Contacts of the helix formed by residues 686 - 698 (chain A) in PDB entry 2FB8
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 686 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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550A MET* 4.0 15.5 - - + -
554A ILE* 4.0 17.3 - - + -
684A ASN 3.6 7.6 - - - +
685A CYS* 1.3 106.6 - - + +
687A LYS* 1.3 60.8 + - - +
688A ALA* 4.2 7.9 - - + +
689A MET* 3.9 17.9 - - + +
690A LYS* 3.3 9.7 + - - +
717A LEU* 4.5 14.4 - - + +
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Residues in contact with LYS 687 (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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685A CYS 4.7 3.8 - - - +
686A PRO* 1.3 72.0 - - - +
688A ALA* 1.3 61.1 + - - +
689A MET 3.3 0.7 - - - -
690A LYS* 3.0 15.7 + - + +
691A ARG* 2.7 44.7 + - - +
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Residues in contact with ALA 688 (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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686A PRO* 3.4 3.3 - - + +
687A LYS* 1.3 79.6 - - - +
689A MET* 1.3 51.0 + - - +
691A ARG* 3.2 28.9 + - - +
692A LEU* 2.7 35.0 + - - +
716A LEU* 5.8 4.5 - - + -
717A LEU* 3.6 26.0 - - + -
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Residues in contact with MET 689 (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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554A ILE* 3.9 18.6 - - + -
557A ALA* 3.8 28.9 - - + -
646A LEU* 3.6 29.6 - - + -
649A LEU* 5.3 0.2 - - + -
650A MET* 3.8 39.5 - - + -
685A CYS* 4.2 2.2 - - - -
686A PRO* 3.9 20.4 + - + +
688A ALA* 1.3 75.3 - - - +
690A LYS* 1.3 67.6 + - - +
692A LEU* 3.5 13.5 - - - +
693A MET* 2.9 25.4 + - - +
714A ILE* 5.0 5.2 - - + -
717A LEU* 3.2 21.1 - - + +
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Residues in contact with LYS 690 (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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678A LEU* 3.1 43.9 + - + +
679A SER* 3.8 15.2 - - - +
681A VAL* 3.8 18.0 - - + +
685A CYS* 4.5 4.0 - - - -
686A PRO 3.3 8.1 + - - +
687A LYS* 3.0 24.8 + - + +
689A MET* 1.3 81.3 - - - +
691A ARG* 1.3 67.2 + - + +
693A MET* 3.2 13.6 + - + +
694A ALA* 3.2 17.1 + - + +
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Residues in contact with ARG 691 (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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687A LYS* 2.7 43.3 + - - +
688A ALA* 3.4 32.4 - - - +
690A LYS* 1.3 71.6 - - + +
692A LEU* 1.3 58.7 + - - +
694A ALA* 3.0 10.9 + - - +
695A GLU* 2.9 33.6 + - + +
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Residues in contact with LEU 692 (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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646A LEU* 3.7 21.3 - - + -
688A ALA 2.7 21.6 + - - +
689A MET* 3.5 13.0 - - - +
691A ARG* 1.3 69.3 - - - +
693A MET* 1.3 67.4 + - - +
695A GLU* 3.1 7.4 + - + +
696A CYS* 2.7 34.9 + - - +
705A PRO* 4.8 7.6 - - + -
709A GLN* 5.9 1.6 - - - +
710A ILE* 4.4 16.4 - - + -
713A SER* 4.1 24.9 - - - +
714A ILE* 3.6 33.9 - - + -
717A LEU* 5.8 2.0 - - + -
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Residues in contact with MET 693 (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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643A GLY* 4.2 3.1 - - - +
646A LEU* 3.4 26.9 - - + +
647A TYR* 3.5 34.5 - - - -
650A MET* 3.9 16.6 - - + -
678A LEU* 4.2 20.2 - - + -
681A VAL* 3.5 32.8 - - + -
685A CYS* 5.5 0.2 - - - -
689A MET 2.9 22.4 + - - +
690A LYS* 3.2 13.9 + - + +
692A LEU* 1.3 72.9 - - - +
694A ALA* 1.3 64.0 + - - +
696A CYS* 2.9 15.9 + - - +
697A LEU* 3.0 24.2 + - + +
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Residues in contact with ALA 694 (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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678A LEU* 4.0 19.9 - - + +
690A LYS 3.2 7.6 + - - +
691A ARG* 3.0 14.4 + - - +
693A MET* 1.3 78.3 - - - +
695A GLU* 1.3 64.5 + - + +
696A CYS 3.0 1.4 + - - -
697A LEU* 3.1 13.4 + - - +
698A LYS* 3.1 21.4 + - + +
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Residues in contact with GLU 695 (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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691A ARG* 2.9 18.2 + - + +
692A LEU* 3.7 10.8 - - + +
694A ALA* 1.3 76.2 - - + +
696A CYS* 1.3 61.9 + - - +
698A LYS* 3.4 34.2 - - - +
703A GLU* 3.9 17.5 - - - +
704A ARG* 3.7 8.8 - - - -
705A PRO* 3.2 29.0 - - + +
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Residues in contact with CYS 696 (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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639A VAL* 3.8 24.4 - - - +
640A TYR* 3.8 5.5 - - - -
642A PHE* 4.3 19.1 - - - -
643A GLY* 4.0 18.4 - - - -
646A LEU* 5.1 0.7 - - - -
692A LEU* 2.7 35.0 + - - +
693A MET* 2.9 10.7 + - - +
695A GLU* 1.3 80.6 - - - +
697A LEU* 1.3 59.2 + - - +
698A LYS 3.4 0.2 - - - -
704A ARG* 3.1 23.6 - - - -
705A PRO* 4.4 10.1 - - - -
710A ILE* 4.4 4.9 - - - -
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Residues in contact with LEU 697 (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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640A TYR* 3.5 53.1 - - + +
643A GLY* 3.6 25.1 - - - +
644A ILE* 3.6 15.3 - - + +
647A TYR* 5.1 2.0 - - + -
676A PRO* 3.4 31.2 - - + -
678A LEU* 4.1 18.8 - - + -
693A MET* 3.0 20.8 + - + +
694A ALA* 3.1 4.0 + - - +
696A CYS* 1.3 76.0 - - - +
698A LYS* 1.3 69.0 + - - +
699A LYS* 3.0 6.4 + - - +
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Residues in contact with LYS 698 (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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694A ALA* 3.1 18.6 + - + +
695A GLU* 3.4 42.2 - - - +
696A CYS 3.4 1.8 + - - -
697A LEU* 1.3 74.9 - - - +
699A LYS* 1.3 68.6 + - - +
700A LYS 3.0 1.9 + - - +
703A GLU* 3.5 51.4 + - + +
704A ARG* 2.8 27.0 + - + +
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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