Contacts of the helix formed by residues 693 - 711 (chain A) in PDB entry 4FE1
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 693 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A SER* 1.3 77.6 - - - +
694A ARG* 1.3 66.0 + - - -
695A GLY 3.2 4.3 + - - -
696A TYR* 3.5 12.9 + - - +
697A TRP* 3.2 16.9 - - - -
724A ILE* 6.5 1.1 - - - -
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Residues in contact with ARG 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A THR* 5.5 0.8 + - - -
693A GLY* 1.3 69.1 - - - -
695A GLY* 1.3 62.6 + - - +
696A TYR 3.3 0.2 - - - -
697A TRP* 3.2 10.0 + - - +
698A GLN* 2.9 60.6 + - - +
720A ARG* 4.3 5.3 - - - +
721A ALA* 2.7 34.1 + - + +
722A LEU 2.8 28.9 + - - +
723A SER* 3.8 5.1 - - - +
724A ILE* 3.5 40.7 - - + +
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Residues in contact with GLY 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693A GLY 3.2 2.0 + - - -
694A ARG* 1.3 83.5 - - - +
696A TYR* 1.3 62.0 + - - +
698A GLN* 3.4 5.4 + - - +
699A GLU* 3.0 33.3 + - - +
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Residues in contact with TYR 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A SER* 6.1 2.5 - - - -
693A GLY 3.5 10.6 + - - +
694A ARG 3.3 0.2 - - - -
695A GLY* 1.3 75.2 - - - +
697A TRP* 1.3 99.1 + + - +
699A GLU* 3.2 14.5 + - - +
700A LEU* 2.9 43.9 + - + +
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Residues in contact with TRP 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A MET* 3.8 40.6 - - + -
692A SER* 3.2 26.6 + - - -
693A GLY 3.2 27.4 - - - -
694A ARG* 3.2 7.7 + - - +
696A TYR* 1.3 97.2 - + - +
698A GLN* 1.3 60.5 + - - +
700A LEU* 3.6 27.9 - - + +
701A ILE* 2.9 38.1 + - + +
721A ALA* 3.9 15.3 - - + -
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Residues in contact with GLN 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A ARG* 2.9 35.4 + - - +
695A GLY* 3.8 6.1 - - - +
697A TRP* 1.3 75.5 - - - +
699A GLU* 1.3 59.3 + - + +
701A ILE* 3.3 8.7 + - - +
702A GLU* 3.0 43.3 + - - +
719A PRO 3.6 19.0 + - - -
720A ARG* 3.3 25.0 - - - +
721A ALA* 3.0 29.7 + - + +
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Residues in contact with GLU 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695A GLY 3.0 22.2 + - - +
696A TYR* 3.5 12.9 - - - +
697A TRP 3.1 0.4 - - - -
698A GLN* 1.3 76.2 - - + +
700A LEU* 1.3 65.0 + - - +
702A GLU* 3.3 31.6 + - - +
703A SER* 3.5 8.3 + - - -
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Residues in contact with LEU 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696A TYR* 2.9 32.2 + - + +
697A TRP* 3.2 36.5 + - + +
699A GLU* 1.3 73.2 - - - +
701A ILE* 1.3 68.9 + - + +
703A SER* 3.0 18.5 + - - -
704A ILE* 3.1 29.4 + - + +
422B ILE* 4.0 22.9 - - + -
426B SER* 4.9 12.6 - - - +
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Residues in contact with ILE 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697A TRP* 2.9 23.6 + - + +
698A GLN* 3.5 10.8 - - - +
700A LEU* 1.3 79.1 - - + +
702A GLU* 1.3 56.6 + - - +
704A ILE* 3.2 14.8 + - + +
705A VAL* 2.8 34.2 + - + +
719A PRO* 3.5 36.1 - - + +
720A ARG 4.0 5.2 - - - +
721A ALA* 3.7 33.2 - - + +
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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 GLN* 3.0 38.9 + - - +
699A GLU* 3.3 23.0 - - - +
700A LEU 3.1 0.4 - - - -
701A ILE* 1.3 76.5 - - - +
703A SER* 1.3 62.4 + - - +
705A VAL* 3.2 10.8 + - + +
706A TRP* 3.0 22.0 + - - +
419B GLU* 5.3 0.2 - - - -
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Residues in contact with SER 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 GLU 3.5 6.6 + - - -
700A LEU 3.0 9.7 + - - -
702A GLU* 1.3 79.0 - - - +
704A ILE* 1.3 62.3 + - - +
706A TRP* 3.5 13.2 - - - +
707A ALA 3.7 0.3 + - - -
418B LYS* 5.6 1.2 - - - +
419B GLU* 3.5 24.9 - - - +
422B ILE* 3.4 47.6 - - - +
423B SER* 3.3 17.9 - - - -
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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
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700A LEU* 3.1 31.0 + - + +
701A ILE* 3.6 16.6 - - + +
702A GLU 3.1 0.2 - - - -
703A SER* 1.3 74.3 - - - +
705A VAL* 1.3 62.2 + - + +
706A TRP 3.1 1.6 - - - -
707A ALA* 3.0 14.0 + - + +
708A HIS* 2.8 45.9 + - + +
423B SER* 4.3 11.4 - - - +
426B SER* 3.8 28.5 - - - +
430B LEU* 5.8 2.9 - - + -
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Residues in contact with VAL 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701A ILE* 2.8 33.0 + - + +
702A GLU* 3.4 10.3 - - + +
704A ILE* 1.3 74.0 - - + +
706A TRP* 1.3 67.2 + - - +
708A HIS* 3.1 11.5 + - + +
709A ASN* 2.9 39.0 + - - +
714A ALA* 4.8 4.4 - - + +
715A PRO* 6.0 2.7 - - + -
719A PRO* 4.2 26.5 - - + +
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Residues in contact with TRP 706 (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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702A GLU 3.0 13.2 + - - +
703A SER 3.5 9.4 - - - +
704A ILE 3.1 0.2 - - - -
705A VAL* 1.3 78.1 - - - +
707A ALA* 1.3 86.6 + - + +
709A ASN* 3.0 10.9 + - + +
710A LYS* 2.9 58.8 + - + +
417B HIS* 6.2 2.0 - - + -
419B GLU* 3.5 34.2 - - + +
420B ALA* 3.7 39.7 - - + -
423B SER* 4.4 3.1 - - - -
424B HIS* 5.6 5.2 - + - -
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Residues in contact with ALA 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 SER 3.7 0.8 + - - -
704A ILE* 3.0 11.0 + - + +
706A TRP* 1.3 91.9 - - + +
708A HIS* 1.3 67.7 + - + +
710A LYS* 3.2 6.0 + - - +
711A LEU* 3.1 30.0 + - + +
423B SER* 4.0 24.7 - - - +
424B HIS* 6.0 2.9 - - + -
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Residues in contact with HIS 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* 2.8 44.8 + - + -
705A VAL* 3.1 11.7 + - + +
707A ALA* 1.3 83.8 - - + +
709A ASN* 1.3 58.2 + - - +
711A LEU 3.2 1.4 + - - -
712A LYS 3.1 3.3 + - - -
713A VAL* 2.7 55.3 + - + +
714A ALA* 3.8 18.4 - - + +
715A PRO* 5.2 5.8 - - + -
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Residues in contact with ASN 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 VAL* 2.9 32.2 + - - +
706A TRP* 3.6 10.7 - - + +
708A HIS* 1.3 71.7 - - - +
710A LYS* 1.3 65.3 + - - +
711A LEU 3.0 2.9 + - - -
712A LYS* 3.3 14.2 + - - +
714A ALA* 3.0 23.4 - - - +
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Residues in contact with LYS 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 TRP* 2.9 43.9 + - + +
707A ALA* 3.2 13.9 + - - +
709A ASN* 1.3 77.1 - - - +
711A LEU* 1.3 69.4 + - + +
712A LYS* 3.5 3.2 + - - +
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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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707A ALA* 3.1 17.4 + - + +
708A HIS* 3.2 0.4 + - - -
709A ASN 3.0 0.4 - - - -
710A LYS* 1.3 93.5 - - + +
712A LYS* 1.3 69.8 + - - +
713A VAL* 3.0 25.2 + - + +
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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