Contacts of the helix formed by residues 702 - 715 (chain A) in PDB entry 4FM9
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 GLU 702 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547A SER* 2.6 37.5 + - - +
550A LYS* 3.1 19.2 + - - +
685A LEU* 4.3 11.6 - - + +
686A TYR* 2.4 31.6 + - - -
693A LEU* 4.6 0.2 - - - +
698A PHE* 2.7 39.0 + - + +
701A LYS* 1.3 73.7 - - - +
703A LEU* 1.3 66.3 + - - +
704A ILE 3.3 1.1 - - - -
705A LEU* 3.1 26.1 + - + +
706A PHE 3.5 2.8 + - - -
1202A GOL 2.9 23.2 + - - +
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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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547A SER* 4.2 11.2 - - - +
548A HIS* 4.1 27.8 - - + -
652A ALA* 3.3 34.1 - - + +
653A PHE* 3.9 19.5 - - + -
664A TRP* 4.5 3.6 - - + -
698A PHE* 3.0 14.8 + - + -
699A ILE* 3.2 35.0 - - + +
702A GLU* 1.3 77.6 - - - +
704A ILE* 1.3 63.3 + - - +
706A PHE* 3.1 24.5 + - + +
707A SER* 3.1 17.0 + - - +
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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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664A TRP* 3.4 69.1 - - + +
665A LEU* 4.3 7.6 - - + -
668A PHE* 3.5 42.2 - - + -
699A ILE 3.0 6.1 + - - -
700A ASN* 3.0 28.9 - - + +
701A LYS 4.0 8.3 - - - +
703A LEU* 1.3 76.4 - - - +
705A LEU* 1.3 67.9 + - - +
707A SER* 3.1 4.0 + - - -
708A ASN* 2.9 23.0 + - - +
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Residues in contact with LEU 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A GLN* 4.9 9.9 - - + -
668A PHE* 3.6 32.8 - - + -
682A GLU* 5.5 6.1 - - - +
701A LYS 3.0 26.2 - - - +
702A GLU* 3.1 17.3 - - + +
704A ILE* 1.3 84.3 - - + +
706A PHE* 1.3 63.8 + - - +
708A ASN* 3.2 3.1 + - - +
709A SER* 2.9 27.2 + - - +
1202A GOL 4.9 19.3 - - - +
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Residues in contact with PHE 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A LYS* 4.3 1.6 - - - -
544A GLN* 3.6 43.8 - - + +
545A ASP* 3.9 12.8 - - - -
547A SER* 4.7 0.9 - - - -
548A HIS* 3.2 53.6 - + + +
702A GLU 3.5 3.2 + - - +
703A LEU* 3.1 17.7 + - + +
705A LEU* 1.3 78.7 - - - +
707A SER* 1.3 65.2 + - - +
709A SER* 2.9 6.6 + - - -
710A ASP* 2.7 53.2 + - + +
713A ARG* 3.9 26.2 - - - -
858A THR* 4.5 8.3 - - - -
7D T 6.0 0.7 - - - -
8D C 5.4 1.6 - - - -
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Residues in contact with SER 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A TRP* 4.1 7.6 - - - -
665A LEU* 3.9 23.6 - - - -
703A LEU* 3.1 15.8 + - - +
704A ILE* 3.1 13.0 + - - -
706A PHE* 1.3 88.8 - - - +
708A ASN* 1.3 58.2 + - - +
710A ASP* 3.2 4.8 + - - +
711A ASN* 2.9 31.9 + - - +
858A THR* 4.0 23.5 + - - +
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Residues in contact with ASN 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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665A LEU* 4.4 6.2 - - + +
668A PHE* 3.6 33.8 - - + -
669A MET* 3.9 22.3 - - + +
672A ARG* 3.4 13.5 + - - +
704A ILE 2.9 9.5 + - - +
705A LEU 3.7 6.8 + - - +
707A SER* 1.3 76.6 - - - +
709A SER* 1.3 60.5 + - - +
711A ASN* 3.2 13.8 + - - +
712A GLU* 2.8 60.6 + - - +
1003A PHE* 5.4 2.1 - - - -
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Residues in contact with SER 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A GLN* 4.3 22.3 + - - +
705A LEU* 2.9 14.7 + - - +
706A PHE* 2.9 14.0 + - - -
708A ASN* 1.3 78.3 + - - +
710A ASP* 1.3 61.1 + - - +
712A GLU* 3.1 11.4 + - - +
713A ARG* 2.8 37.9 + - - +
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Residues in contact with ASP 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A PHE* 2.7 37.0 + - + +
707A SER* 3.3 11.4 - - - +
709A SER* 1.3 71.6 - - - +
711A ASN* 1.3 53.6 + - - +
713A ARG* 3.2 23.9 + - - +
714A SER* 2.6 66.5 + - - -
856A ILE 4.0 1.7 - - - +
857A GLY* 3.4 16.0 - - - +
858A THR* 3.2 18.5 + - - +
10C G 5.3 1.9 + - - -
11C A 5.6 1.6 - - - +
7D T 5.7 0.3 - - - +
8D C 4.2 10.5 - - - +
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Residues in contact with ASN 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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665A LEU* 3.3 18.6 - - - +
669A MET* 5.6 2.6 - - - -
707A SER 2.9 11.3 + - - +
708A ASN* 3.3 13.8 + - - +
710A ASP* 1.3 76.1 - - - +
712A GLU* 1.3 57.7 + - - +
714A SER* 4.4 3.6 - - - -
715A ILE* 2.8 34.7 + - + +
857A GLY* 3.5 4.6 - - - -
858A THR 2.9 30.6 + - - +
860A TRP* 3.1 32.5 - - - +
1003A PHE* 3.5 20.7 - - + -
1009A LEU* 4.1 8.6 - - + +
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Residues in contact with GLU 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A ARG* 2.7 35.5 + - - -
708A ASN* 2.8 36.7 + - - +
709A SER* 3.1 10.9 + - - +
711A ASN* 1.3 73.7 - - - +
713A ARG* 1.3 58.7 + - - +
715A ILE 3.9 6.9 - - - +
724A PRO* 3.3 26.5 - - + +
1003A PHE* 4.0 23.6 - - + -
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Residues in contact with ARG 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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489A LYS* 4.2 4.4 - - - +
545A ASP* 3.2 36.4 + - - -
706A PHE* 3.9 20.0 - - - -
709A SER* 2.8 17.5 + - - +
710A ASP* 3.2 29.7 + - - +
712A GLU* 1.3 76.5 - - - +
714A SER* 1.3 64.6 + - - +
723A LYS* 3.4 20.6 - - - +
724A PRO* 4.4 11.4 - - + +
759A HIS* 4.8 9.7 - - - +
11C A 3.6 22.1 + - - +
12C T 3.6 60.2 + - - +
7D T 5.6 1.4 + - - -
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Residues in contact with SER 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 ASP* 2.6 44.6 + - - -
711A ASN* 4.0 1.3 - - - -
713A ARG* 1.3 79.3 + - - +
715A ILE* 1.3 61.2 + - - +
716A PRO* 3.8 0.7 - - - +
723A LYS* 3.3 25.0 - - - -
855A GLY* 3.7 12.2 - - - -
856A ILE 2.9 32.8 + - - -
857A GLY* 4.1 2.7 - - - -
10C G 4.9 2.1 + - - -
11C A 4.8 9.7 + - - -
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Residues in contact with ILE 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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711A ASN* 2.8 27.0 + - - +
712A GLU 3.9 8.0 - - - +
714A SER* 1.3 80.5 - - - +
716A PRO* 1.3 81.9 - - + +
723A LYS* 4.8 1.6 - - - -
724A PRO* 5.2 1.4 - - - +
855A GLY* 4.9 7.2 - - - -
857A GLY 5.0 1.6 - - - +
860A TRP* 3.8 35.9 - - + +
861A SER 4.6 2.2 - - - +
862A CYS* 4.4 11.0 - - + -
1001A VAL* 3.1 33.9 - - + +
1003A PHE* 3.3 26.5 - - + -
1009A LEU* 4.0 14.1 - - + -
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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