Contacts of the helix formed by residues 698 - 710 (chain A) in PDB entry 1GM5
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 698 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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697A VAL* 1.3 86.6 - - - +
699A GLU* 1.3 58.4 + - - -
700A GLU 3.6 0.9 - - - -
701A ALA* 2.7 8.5 + - - +
702A MET* 2.3 45.0 + - - +
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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
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698A GLY* 1.3 68.0 - - - +
700A GLU* 1.3 61.8 + - + +
702A MET* 4.4 2.2 - - - +
703A GLU* 1.9 60.4 + - - +
706A ARG* 6.2 0.3 - - - -
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Residues in contact with GLU 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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698A GLY 3.6 0.6 - - - -
699A GLU* 1.3 79.8 - - + +
701A ALA* 1.3 61.5 + - - +
703A GLU* 2.3 40.1 - - - +
704A ARG* 2.8 35.8 + - - +
724A THR* 5.0 7.8 - - - +
18Y C 5.7 4.9 - - - +
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Residues in contact with ALA 701 (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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667A GLU* 5.1 9.6 - - + -
697A VAL* 3.6 32.8 - - + -
698A GLY 2.7 15.4 + - - +
700A GLU* 1.3 71.4 - - - +
702A MET* 1.3 55.6 + - + +
704A ARG* 2.2 54.6 + - - +
705A LEU* 3.3 6.9 + - + +
18Y C 5.8 1.6 - - - +
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Residues in contact with MET 702 (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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558A LEU* 6.1 6.3 - - + -
694A VAL* 3.5 37.0 - - + -
696A ASP* 2.6 33.2 - - - +
697A VAL* 3.6 7.4 - - + +
698A GLY* 2.3 35.2 + - - +
699A GLU* 4.1 2.5 - - - +
701A ALA* 1.3 63.5 - - + +
703A GLU* 1.3 65.5 + - - +
704A ARG 2.8 2.5 - - - -
705A LEU* 4.1 16.3 - - + +
706A ARG* 2.9 28.9 + - + +
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Residues in contact with GLU 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* 1.9 54.7 + - - +
700A GLU* 2.3 34.4 - - - +
702A MET* 1.3 67.5 - - - +
704A ARG* 1.3 61.6 + - - +
706A ARG* 3.7 8.7 - - - +
707A PHE* 3.4 14.9 + - - +
720A TYR* 3.7 17.3 + - - +
724A THR* 5.0 6.2 - - - +
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Residues in contact with ARG 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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667A GLU* 3.1 26.3 + - + -
671A LEU* 4.1 10.3 - - + -
700A GLU* 2.8 22.6 + - - +
701A ALA* 2.2 40.8 + - - +
703A GLU* 1.3 78.5 + - - +
705A LEU* 1.3 57.0 + - + +
707A PHE* 2.4 30.8 + - - +
708A PHE* 2.7 13.9 + - - -
720A TYR* 3.6 15.7 + - + +
724A THR* 2.7 28.7 - - - +
725A ARG* 1.5 72.5 - - - +
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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
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558A LEU* 4.7 10.5 - - + -
666A PRO* 4.9 16.2 - - + -
667A GLU* 4.5 20.6 - - + -
671A LEU* 4.7 2.0 - - + +
674A LEU* 4.0 26.7 - - + -
692A LEU* 4.7 17.0 - - + -
694A VAL* 5.1 13.2 - - + -
701A ALA* 3.3 8.5 + - + +
702A MET* 3.8 28.0 - - + +
704A ARG* 1.3 77.0 - - + +
706A ARG* 1.3 65.0 + - - +
708A PHE* 2.8 22.8 + - + +
709A THR* 2.9 20.2 + - + +
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Residues in contact with ARG 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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558A LEU* 4.3 16.2 - - + +
699A GLU* 6.2 0.2 - - - -
702A MET* 2.9 21.5 + - + +
703A GLU* 3.7 8.1 - - - +
705A LEU* 1.3 73.3 - - - +
707A PHE* 1.3 61.6 + - - +
709A THR* 2.7 22.4 + - - +
710A LEU* 3.7 8.1 + - - +
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Residues in contact with PHE 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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671A LEU* 4.2 11.2 - - + -
703A GLU 3.6 10.5 - - - +
704A ARG 2.4 28.9 + - - +
706A ARG* 1.3 72.0 - - - +
708A PHE* 1.3 72.0 + - - +
710A LEU* 3.2 7.9 + - - +
711A ASN* 1.9 62.5 + - + -
716A LYS* 3.7 13.2 - - + -
717A ILE* 4.6 3.6 - - + -
720A TYR* 3.5 61.7 - + + +
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Residues in contact with PHE 708 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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556A THR* 4.5 4.3 - - + -
663A ILE* 5.3 1.8 - - + -
671A LEU* 4.2 15.0 - - + -
674A LEU* 3.4 52.5 - - + -
675A HIS* 4.5 2.2 - - + -
678A ARG* 1.3 85.2 + - + -
692A LEU* 4.6 15.0 - - + -
704A ARG 2.7 7.6 + - - +
705A LEU* 3.0 20.0 - - + +
707A PHE* 1.3 84.1 - - - +
709A THR* 1.3 56.7 + - + +
711A ASN* 2.5 32.4 + - - +
717A ILE* 5.0 7.0 - - + -
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Residues in contact with THR 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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556A THR* 4.0 41.7 + - + +
557A MET 4.9 0.4 - - - -
558A LEU* 3.8 37.6 - - + +
678A ARG* 5.0 2.6 + - - -
692A LEU* 5.1 7.0 - - + -
705A LEU 3.2 15.3 - - - +
706A ARG* 2.7 25.8 + - - +
708A PHE* 1.3 84.9 - - + +
710A LEU* 1.3 59.9 + - - +
711A ASN 3.3 1.0 + - - -
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Residues in contact with LEU 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 ARG 3.7 9.4 + - - +
707A PHE* 3.2 3.6 + - - +
708A PHE 2.9 1.2 + - - -
709A THR* 1.3 81.4 + - - +
711A ASN* 1.3 70.0 + - - +
712A THR* 3.5 14.7 + - - +
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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