Contacts of the strand formed by residues 707 - 716 (chain A) in PDB entry 1FO4
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 PHE 707 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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701A ALA 4.1 0.9 - - - -
702A ILE* 3.9 34.3 - - + -
705A ASN* 3.3 39.4 + - - -
706A SER* 1.3 81.4 - - - +
708A TYR* 1.3 68.1 + - - +
709A GLY 3.8 3.2 + - - +
864A TYR* 4.5 4.9 - + - -
871A ARG* 5.4 0.7 + - - -
899A ARG* 3.7 57.7 - - + +
900A LEU 3.1 18.8 - - - +
901A CYS* 4.1 22.0 - - - -
902A LYS* 3.9 10.0 - - - +
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Residues in contact with TYR 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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651A ASP* 4.4 1.6 - - - -
707A PHE* 1.3 72.5 - - - +
709A GLY* 1.3 64.6 + - - +
710A SER 4.5 2.9 - - - +
867A ALA* 3.9 19.3 - - + -
868A GLY 2.7 29.8 + - - -
869A ASN* 2.9 7.0 + - - -
870A SER* 2.7 34.5 + - - -
871A ARG* 3.5 53.6 - - + +
875A HIS* 5.4 1.4 + - - -
899A ARG* 4.7 0.3 + - - -
900A LEU* 3.0 41.7 + - + +
902A LYS* 3.5 44.2 - - + +
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Residues in contact with GLY 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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707A PHE* 3.8 5.9 + - - +
708A TYR* 1.3 74.9 - - - +
710A SER* 1.3 53.3 + - - -
871A ARG* 4.7 9.0 - - - +
875A HIS* 6.2 2.2 - - - -
899A ARG* 2.6 25.6 + - - -
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Residues in contact with SER 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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708A TYR 4.5 2.9 - - - +
709A GLY* 1.3 74.9 - - - -
711A GLU* 1.3 69.5 + - - +
712A LEU* 3.6 6.6 + - - +
875A HIS* 4.9 8.1 - - - -
898A GLY 4.4 2.1 - - - +
899A ARG* 3.4 12.2 + - - +
900A LEU* 5.8 2.4 + - - +
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Residues in contact with GLU 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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710A SER* 1.3 83.6 + - - +
712A LEU* 1.3 76.4 + - - +
713A LYS* 4.0 16.4 + - + +
862A ASP* 5.1 0.5 - - - +
895A ARG* 4.9 2.8 + - - -
897A THR* 3.6 31.4 + - - +
898A GLY 3.5 11.9 - - - +
899A ARG* 3.6 24.2 + - + +
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Residues in contact with LEU 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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710A SER 3.6 2.4 + - - +
711A GLU* 1.3 78.1 - - - +
713A LYS* 1.3 65.5 + - - +
875A HIS* 3.5 41.3 - - + +
878A MET* 3.6 32.1 - - + -
879A GLU* 3.8 28.0 - - + +
882A LEU* 3.6 14.1 - - + -
897A THR* 3.0 5.2 - - - -
898A GLY* 2.8 35.9 + - - +
900A LEU* 5.2 2.2 - - + -
1142A PHE* 4.6 15.7 - - + -
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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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711A GLU* 4.0 14.5 + - + +
712A LEU* 1.3 81.0 - - - +
714A ILE* 1.3 79.8 + - - +
715A GLU* 3.4 23.9 + - + +
882A LEU* 3.9 2.3 - - - +
895A ARG* 3.5 30.1 - - + +
896A GLY 3.3 11.9 - - - +
897A THR* 4.0 7.0 - - + -
1142A PHE* 3.5 19.8 - - - +
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Residues in contact with ILE 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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713A LYS* 1.3 81.8 - - - +
715A GLU* 1.3 64.4 + - - +
882A LEU* 3.7 35.4 - - + +
883A PHE* 4.1 23.8 - - + -
885A MET* 5.2 2.4 - - - +
894A ILE* 4.2 1.9 - - + +
895A ARG* 3.6 0.9 - - - -
896A GLY 3.0 30.0 + - - +
954A HIS* 3.9 40.6 - - + +
955A PHE* 4.5 1.3 - - + -
1140A TYR* 4.2 14.8 - - - +
1142A PHE* 3.5 23.3 - - + -
1145A ASN* 4.4 4.9 - - - +
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Residues in contact with GLU 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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713A LYS* 3.4 26.6 + - + +
714A ILE* 1.3 79.0 - - - +
716A LYS* 1.3 68.8 + - - +
717A GLY 5.4 4.6 - - - +
719A LEU* 3.8 13.6 + - + +
894A ILE* 3.4 8.1 - - - +
895A ARG* 3.2 37.4 + - + -
1145A ASN* 3.7 14.3 - - - +
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Residues in contact with LYS 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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715A GLU* 1.3 78.9 - - - +
717A GLY* 1.3 68.5 + - - +
719A LEU* 5.4 1.0 + - - +
890A LYS* 5.4 5.1 - - - +
891A ILE 5.3 2.7 - - - +
892A PRO* 3.4 9.4 - - - +
893A ASN* 3.3 2.1 - - - -
894A ILE* 2.9 44.8 + - + +
952A LEU* 4.1 17.2 + - - +
953A THR 3.2 14.6 + - - -
954A HIS* 3.6 30.5 - - + +
956A ASN* 2.9 27.0 + - - +
1145A ASN* 4.4 2.9 - - - +
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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