Contacts of the helix formed by residues 696 - 714 (chain A) in PDB entry 4XK8
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 696 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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695A SER* 1.3 78.5 - - - +
697A ARG* 1.3 62.8 + - - -
698A GLY 3.2 4.1 + - - -
699A TYR* 3.6 11.9 + - - +
700A TRP* 3.0 18.5 + - - -
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Residues in contact with ARG 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696A GLY* 1.3 69.7 - - - -
698A GLY* 1.3 62.8 + - - +
699A TYR 3.4 0.2 - - - -
700A TRP* 3.8 10.3 - - - -
701A GLN* 2.9 67.1 + - - +
723A ARG* 4.3 6.7 - - - +
724A ALA* 2.9 31.0 + - + +
725A LEU 2.8 32.0 + - - +
726A SER* 4.1 4.1 - - - +
727A ILE* 4.0 33.3 - - + +
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Residues in contact with GLY 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696A GLY 3.2 1.8 + - - -
697A ARG* 1.3 79.7 - - - +
699A TYR* 1.3 65.2 + - - +
701A GLN* 3.1 6.8 + - - +
702A GLU* 3.0 32.2 + - - +
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Residues in contact with TYR 699 (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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695A SER* 6.2 1.3 - - - -
696A GLY 3.6 10.6 + - - +
698A GLY* 1.3 74.1 - - - +
700A TRP* 1.3 98.6 + + + +
702A GLU* 3.2 13.4 + - - +
703A LEU* 2.9 45.4 + - + +
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Residues in contact with TRP 700 (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 MET* 3.6 41.5 - - + -
692A PHE* 6.0 0.8 - - - +
695A SER* 3.0 27.7 + - - -
696A GLY 3.0 29.7 + - - -
697A ARG* 3.5 7.8 + - - +
698A GLY 3.2 0.4 - - - -
699A TYR* 1.3 102.4 - + - +
701A GLN* 1.3 57.4 + - - +
703A LEU* 3.5 20.1 + - + +
704A ILE* 2.9 40.1 + - + +
724A ALA* 4.0 11.7 - - + -
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Residues in contact with GLN 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697A ARG* 2.9 46.2 + - - +
698A GLY* 3.1 8.0 + - - +
700A TRP* 1.3 77.4 - - - +
702A GLU* 1.3 58.8 + - + +
704A ILE* 3.3 8.3 + - - +
705A GLU* 2.9 37.3 + - - +
722A PRO 3.9 3.4 + - - +
723A ARG* 3.2 29.0 + - - +
724A ALA* 3.0 27.1 - - + +
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Residues in contact with GLU 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698A GLY 3.0 16.9 + - - +
699A TYR* 3.2 12.3 + - - +
701A GLN* 1.3 74.7 - - + +
703A LEU* 1.3 66.0 + - - +
705A GLU* 2.9 33.7 + - - +
706A SER* 3.1 14.7 + - - -
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Residues in contact with LEU 703 (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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699A TYR* 2.9 36.3 + - + +
700A TRP* 3.7 32.1 - - + +
702A GLU* 1.3 74.7 - - - +
704A ILE* 1.3 60.0 + - + +
706A SER* 3.1 8.7 + - - -
707A ILE* 3.0 45.0 + - + +
419B ILE* 3.8 26.9 - - + +
423B SER* 4.6 18.6 - - - +
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Residues in contact with ILE 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700A TRP* 2.9 28.5 + - + +
701A GLN* 3.4 11.2 - - - +
703A LEU* 1.3 78.9 - - + +
705A GLU* 1.3 56.3 + - - +
707A ILE* 3.9 12.9 - - + +
708A VAL* 2.9 32.6 + - + +
722A PRO* 3.4 35.9 - - + +
723A ARG 3.9 6.1 - - - +
724A ALA* 3.7 33.4 - - + +
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Residues in contact with GLU 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701A GLN* 2.9 29.6 + - - +
702A GLU* 2.9 27.4 + - - +
704A ILE* 1.3 77.5 - - - +
706A SER* 1.3 63.2 + - - +
708A VAL* 3.3 7.8 + - - +
709A TRP* 3.0 21.8 + - - +
416B GLU* 5.2 2.5 - - + -
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Residues in contact with SER 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A GLU 3.1 10.5 + - - -
703A LEU 3.1 8.0 + - - -
705A GLU* 1.3 77.2 - - - +
707A ILE* 1.3 63.3 + - - +
709A TRP* 3.1 7.6 + - - +
710A ALA 3.0 17.2 + - - -
415B LYS* 5.8 0.5 - - - +
416B GLU* 3.9 26.0 - - - +
419B ILE* 3.5 45.7 - - - +
420B SER* 3.9 10.7 - - - -
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Residues in contact with ILE 707 (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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703A LEU* 3.0 34.8 + - + +
704A ILE* 3.9 13.0 - - + +
706A SER* 1.3 76.8 - - - +
708A VAL* 1.3 58.4 + - + +
710A ALA* 3.0 10.0 + - + +
711A HIS* 2.8 56.7 + - + -
420B SER* 4.5 6.7 - - - +
423B SER* 3.8 27.8 - - - +
427B LEU* 6.2 2.0 - - + -
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Residues in contact with VAL 708 (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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704A ILE* 2.9 34.0 + - + +
705A GLU* 3.5 7.9 - - - +
707A ILE* 1.3 72.8 - - + +
709A TRP* 1.3 67.4 + - - +
711A HIS* 3.1 9.7 + - + +
712A ASN* 2.9 36.9 + - - +
717A ALA* 4.7 6.0 - - + +
718A PRO* 6.0 1.8 - - + -
722A PRO* 4.0 33.0 - - + +
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Residues in contact with TRP 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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705A GLU 3.0 13.2 + - - +
706A SER 3.1 9.4 + - - +
708A VAL* 1.3 76.1 - - - +
710A ALA* 1.3 92.8 + - + +
712A ASN* 3.1 11.9 + - + +
713A LYS* 3.0 52.9 + - + +
414B HIS* 6.1 3.6 - - + -
416B GLU* 3.5 45.9 + - + +
417B ALA* 3.6 32.3 - - + -
420B SER* 4.1 3.6 - - - -
421B HIS* 5.3 5.8 - + - -
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Residues in contact with ALA 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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706A SER 3.0 4.6 + - - -
707A ILE* 3.0 12.8 + - + +
709A TRP* 1.3 88.0 - - + +
711A HIS* 1.3 65.5 + - + +
713A LYS* 3.4 15.1 + - - +
714A LEU* 3.6 13.3 + - - +
420B SER* 3.8 28.7 - - - +
421B HIS* 6.1 2.0 - - + -
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Residues in contact with HIS 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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707A ILE* 2.8 49.0 + - + +
708A VAL* 3.1 10.9 + - + +
710A ALA* 1.3 76.8 - - + +
712A ASN* 1.3 64.3 + - - +
714A LEU 3.2 2.1 + - - -
715A LYS 3.2 3.5 + - - -
716A VAL* 2.9 63.1 + - + +
717A ALA* 4.0 10.1 - - + -
718A PRO* 5.1 5.8 - - + -
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Residues in contact with ASN 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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708A VAL* 2.9 28.1 + - - +
709A TRP* 3.1 12.7 + - + +
711A HIS* 1.3 73.4 - - - +
713A LYS* 1.3 67.0 + - - +
715A LYS* 3.0 19.2 + - - +
717A ALA* 3.3 20.9 - - - +
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Residues in contact with LYS 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 TRP* 3.0 46.6 + - + +
710A ALA* 3.5 13.7 - - - +
711A HIS 3.3 0.2 - - - -
712A ASN* 1.3 77.0 - - - +
714A LEU* 1.3 67.6 + - + +
715A LYS* 3.4 4.3 + - - +
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Residues in contact with LEU 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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710A ALA 3.6 9.6 + - - +
711A HIS 3.2 2.8 + - - +
712A ASN 3.1 0.6 - - - -
713A LYS* 1.3 87.5 - - + +
715A LYS* 1.3 72.5 + - - +
716A VAL* 3.2 25.7 + - + +
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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