Contacts of the helix formed by residues 677 - 689 (chain A) in PDB entry 4FLZ
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 GLY 677 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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675A ALA 3.3 8.1 + - - -
676A ILE* 1.3 76.0 - - - +
678A PRO* 1.4 76.6 - - - +
679A HIS* 3.3 11.4 - - - -
680A VAL* 3.0 17.6 + - - +
681A ALA* 3.1 10.6 + - - +
711A SER* 3.3 2.2 - - - -
14T C 4.0 11.1 - - - -
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Residues in contact with PRO 678 (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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664A GLU* 4.4 4.7 - - - +
677A GLY* 1.4 80.4 - - - +
679A HIS* 1.4 60.9 + - - +
681A ALA* 3.3 3.2 + - + +
682A VAL* 3.1 30.0 + - - +
701A TYR* 3.4 37.0 - - + +
703A VAL* 5.7 0.2 - - + -
710A ILE* 3.5 28.7 - - + +
711A SER* 3.3 27.8 - - - +
714A ALA* 3.9 12.6 - - + -
13T T 4.0 13.2 - - - +
14T C 4.6 0.2 - - - -
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Residues in contact with HIS 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A GLU* 3.5 32.3 + - + -
665A GLN 3.1 17.4 + - - -
666A ILE* 3.4 21.6 - - + +
677A GLY* 3.3 8.6 - - - -
678A PRO* 1.4 78.3 - - - +
680A VAL* 1.3 76.0 + - + +
682A VAL* 4.5 0.2 - - - -
683A ALA* 3.0 26.9 + - - +
699A ILE* 3.6 18.5 - - + +
701A TYR* 3.7 27.5 - - + -
5P C 4.1 5.2 - - - -
6P A 2.9 42.0 + - - -
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Residues in contact with VAL 680 (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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666A ILE* 4.3 1.3 - - + -
670A LEU* 4.4 4.9 - - + -
673A TYR* 3.7 50.7 - - + -
675A ALA 4.8 0.2 - - - +
676A ILE* 3.8 24.2 - - + -
677A GLY 3.0 15.1 + - - +
679A HIS* 1.3 100.8 - - + +
681A ALA* 1.3 57.7 + - - +
682A VAL 3.3 1.6 - - - -
683A ALA* 3.5 6.4 - - - +
684A LYS* 2.8 39.1 + - - +
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Residues in contact with ALA 681 (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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676A ILE* 3.6 16.7 - - + +
677A GLY 3.1 11.2 + - - +
678A PRO 3.6 6.7 - - - +
680A VAL* 1.3 75.8 - - - +
682A VAL* 1.4 60.2 + - - +
684A LYS* 3.5 6.7 + - - +
685A ARG* 3.4 31.3 + - - +
711A SER* 3.4 31.6 - - - +
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Residues in contact with VAL 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678A PRO 3.1 19.3 + - - +
679A HIS 3.7 4.7 - - - +
681A ALA* 1.4 72.9 - - - +
683A ALA* 1.4 58.8 + - - +
685A ARG* 3.3 15.3 + - - +
686A LEU* 3.1 30.3 + - + +
699A ILE* 3.6 21.5 - - + -
701A TYR* 4.0 11.0 - - + -
714A ALA* 3.7 37.2 - - + +
715A ILE 4.1 2.7 - - - -
716A ALA* 3.7 31.4 - - + +
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Residues in contact with ALA 683 (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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666A ILE* 3.6 26.7 - - + -
670A LEU* 3.8 15.0 - - + -
679A HIS 3.0 19.2 + - - +
680A VAL 3.3 5.1 + - - +
682A VAL* 1.4 73.0 - - - +
684A LYS* 1.4 59.6 + - - +
686A LEU* 3.2 14.1 + - - +
687A ALA* 3.0 28.9 + - - +
693A VAL* 3.6 7.5 - - + +
699A ILE* 4.2 6.7 - - + -
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Residues in contact with LYS 684 (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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670A LEU* 4.0 39.0 + - + -
671A SER* 5.7 2.0 - - - +
676A ILE* 3.5 40.6 - - + +
680A VAL* 2.8 27.1 + - + +
681A ALA* 3.7 6.5 - - - +
682A VAL 3.4 0.2 - - - -
683A ALA* 1.4 71.0 - - - +
685A ARG* 1.3 58.2 + - - +
687A ALA* 3.3 3.9 + - - +
688A ALA* 2.9 29.4 + - - +
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Residues in contact with ARG 685 (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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681A ALA* 3.4 22.2 + - - +
682A VAL* 3.3 23.2 + - - +
683A ALA 3.3 0.6 - - - -
684A LYS* 1.3 77.6 - - - +
686A LEU* 1.4 61.4 + - + +
688A ALA* 3.4 10.1 - - + +
689A LYS* 3.2 20.4 + - - +
711A SER 3.8 17.6 + - - -
712A LYS* 4.7 7.3 + - - +
714A ALA 2.9 32.3 + - - +
715A ILE* 4.1 8.3 - - - +
716A ALA* 4.7 2.0 - - - +
719A GLU* 4.8 16.8 + - - +
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Residues in contact with LEU 686 (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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682A VAL* 3.1 29.1 + - + +
683A ALA* 3.2 7.6 + - - +
685A ARG* 1.4 73.3 - - + +
687A ALA* 1.4 65.7 + - - +
689A LYS* 3.0 16.7 + - + +
691A VAL* 3.0 48.2 + - + +
693A VAL* 4.4 3.1 - - + -
697A MET* 6.0 1.1 - - - -
699A ILE* 4.1 26.0 - - + -
716A ALA* 4.3 18.2 - - + -
718A GLU* 6.4 1.8 - - + -
719A GLU* 4.4 12.8 - - + +
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Residues in contact with ALA 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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670A LEU* 3.9 18.8 - - + -
683A ALA 3.0 14.0 + - - +
684A LYS* 3.3 8.3 + - - +
686A LEU* 1.4 74.5 - - - +
688A ALA* 1.4 54.4 + - - +
690A GLY* 2.9 25.3 + - - -
691A VAL 3.4 15.0 + - - +
693A VAL* 3.9 8.4 - - + +
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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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684A LYS 2.9 13.8 + - - +
685A ARG* 3.4 14.6 - - + +
687A ALA* 1.4 74.7 - - - +
689A LYS* 1.4 57.4 + - - +
690A GLY 3.3 1.0 + - - -
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Residues in contact with LYS 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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685A ARG 3.2 11.5 + - - +
686A LEU* 3.0 17.8 + - + +
688A ALA* 1.4 74.5 - - - +
690A GLY* 1.3 56.9 + - - +
691A VAL* 4.8 6.0 - - + +
719A GLU* 5.9 3.1 - - - +
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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