Contacts of the helix formed by residues 718 - 729 (chain A) in PDB entry 3F7F
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 SER 718 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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716A GLU* 3.3 4.2 + - - +
717A ASN* 1.3 79.4 + - - +
719A PHE* 1.3 66.2 + - - +
720A PHE* 3.3 14.2 + - - +
721A MET* 3.1 23.0 + - - +
722A THR* 3.2 14.8 + - - -
682B ASP* 5.5 2.2 - - - -
712B ALA* 4.1 10.8 - - - -
713B SER 3.1 34.8 + - - -
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Residues in contact with PHE 719 (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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718A SER* 1.3 74.3 - - - +
720A PHE* 1.3 102.1 + + - +
722A THR* 3.6 8.4 - - - -
723A PHE* 2.9 26.0 + - - +
664B LEU* 3.9 11.9 - - + -
667B LEU* 4.5 1.8 - - + -
675B LEU* 4.4 6.1 - - + -
678B VAL* 3.7 36.3 - - + +
679B LEU* 3.7 22.4 - - + -
682B ASP* 3.7 27.2 + - - +
708B ASN 3.7 11.0 - - - -
709B VAL* 3.9 19.1 - - + -
712B ALA* 3.6 26.9 - - + -
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Residues in contact with PHE 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718A SER* 3.0 8.9 + - - +
719A PHE* 1.3 114.5 - + - +
721A MET* 1.3 63.9 + - - +
723A PHE* 3.4 5.3 + - - +
724A PHE* 3.0 42.1 + + + -
660B LYS* 4.0 19.3 - - + -
663B LEU* 3.7 31.0 - - + -
664B LEU* 3.9 11.9 - - - -
667B LEU* 3.8 12.6 - - + -
709B VAL* 4.0 15.0 - - + -
712B ALA* 3.6 28.7 - - + -
713B SER 4.1 6.5 - - - +
714B ILE* 4.2 17.0 - - + -
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Residues in contact with MET 721 (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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716A GLU* 3.7 14.1 - - + +
717A ASN* 2.7 31.6 - - - +
718A SER* 3.1 17.7 + - - +
720A PHE* 1.3 81.5 - - - +
722A THR* 1.3 59.0 + - - +
724A PHE* 3.4 27.6 + - + +
725A ARG* 3.0 29.1 + - - +
713B SER 4.5 5.8 - - - +
714B ILE* 5.0 5.6 - - - -
715B THR 4.4 10.5 - - - +
716B GLU* 4.6 5.8 - - + -
721B MET* 3.2 54.3 - - + +
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Residues in contact with THR 722 (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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716A GLU* 3.1 34.4 + - - +
718A SER 3.2 9.6 + - - -
719A PHE* 3.6 11.4 - - - -
720A PHE 3.3 0.2 - - - -
721A MET* 1.3 73.2 - - - +
723A PHE* 1.3 66.8 - - - +
725A ARG* 3.5 5.8 + - - +
726A SER* 3.0 35.5 + - - +
678B VAL* 3.7 21.3 - - + -
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Residues in contact with PHE 723 (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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719A PHE 2.9 18.1 + - - +
720A PHE 3.5 4.5 - - - +
722A THR* 1.3 73.7 - - - +
724A PHE* 1.3 76.5 + + - +
726A SER* 3.1 2.6 + - - -
727A TYR* 2.9 43.5 + + + +
667B LEU* 3.5 62.6 - - + -
670B GLN* 4.3 6.1 - - + -
671B ASP* 3.8 19.3 - - + -
674B LEU* 3.4 34.5 - - + +
675B LEU* 3.7 22.9 - - - -
678B VAL* 4.1 11.2 - - + -
728B ILE* 4.5 4.9 - - + -
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Residues in contact with PHE 724 (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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720A PHE* 3.0 27.8 + - + -
721A MET* 3.4 36.8 - - + +
723A PHE* 1.3 82.5 - + - +
725A ARG* 1.3 61.8 + - - +
727A TYR* 3.2 3.1 + - - +
728A ILE* 3.0 23.9 + - - +
663B LEU* 4.2 22.4 - - + -
667B LEU* 3.9 22.2 - - + -
716B GLU* 5.9 0.4 - - - -
724B PHE* 3.4 30.1 - - + -
725B ARG* 3.8 29.6 - - + -
728B ILE* 3.5 34.8 - - + -
729B ILE* 5.3 0.9 - - + -
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Residues in contact with ARG 725 (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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537A THR* 3.5 36.0 + - - +
539A GLU* 4.7 8.7 + - - -
659A TYR* 3.1 20.4 - - + +
663A LEU* 5.3 1.1 - - + -
716A GLU* 3.0 40.2 + - - +
721A MET 3.0 13.3 + - - +
722A THR* 3.9 7.6 - - - +
724A PHE* 1.3 80.3 - - - +
726A SER* 1.3 85.9 + - - +
729A ILE* 2.6 56.9 + - + +
724B PHE* 3.8 31.8 - - + -
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Residues in contact with SER 726 (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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722A THR* 3.0 24.3 + - - +
723A PHE 3.7 2.5 - - - -
725A ARG* 1.3 100.2 + - - +
727A TYR* 1.3 64.1 + - - +
729A ILE* 3.5 17.2 - - - +
674B LEU* 3.8 25.7 - - - +
677B GLU* 5.2 1.7 + - - -
678B VAL* 5.1 0.2 - - - +
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Residues in contact with TYR 727 (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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400A LYS* 5.3 2.1 + - - -
723A PHE* 2.9 36.3 + + + +
724A PHE 3.5 3.8 - - - +
726A SER* 1.3 80.7 - - - +
728A ILE* 1.3 63.6 + - + +
729A ILE* 4.8 0.2 - - - +
670B GLN* 3.0 59.5 + - + +
671B ASP* 3.9 19.1 - - + -
674B LEU* 4.0 7.0 - - + -
727B TYR* 6.0 4.7 - + - -
728B ILE* 3.9 20.4 - - + -
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Residues in contact with ILE 728 (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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400A LYS* 2.8 28.0 + - - +
666A ASN* 3.4 17.2 + - - +
667A LEU* 4.2 9.2 - - + -
670A GLN* 3.9 10.1 - - - +
724A PHE 3.0 15.9 + - - +
725A ARG 4.1 0.7 - - - +
727A TYR* 1.3 82.8 - - + +
729A ILE* 1.3 63.1 + - - +
723B PHE* 4.5 5.2 - - + -
724B PHE* 3.5 52.0 - - + +
727B TYR* 3.9 33.2 - - + -
728B ILE* 4.4 10.1 - - + -
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Residues in contact with ILE 729 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A LYS* 3.3 13.7 + - - -
533A LEU* 3.8 24.7 - - + -
537A THR* 5.1 3.4 - - + -
659A TYR* 4.1 18.6 - - + +
662A PHE* 3.8 20.8 - - + -
663A LEU* 3.3 33.2 - - + -
666A ASN* 4.2 11.4 - - - +
725A ARG* 2.6 51.4 + - + +
726A SER* 3.5 15.6 - - - +
727A TYR 4.8 0.5 - - - +
728A ILE* 1.3 81.6 - - - +
724B PHE* 5.8 1.3 - - + -
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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