Contacts of the helix formed by residues 714 - 724 (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 714 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397A ASP* 4.0 13.9 + - - -
526A PRO* 4.0 17.9 - - - +
675A HIS* 3.6 22.5 + - - -
713A ASP* 1.3 74.7 + - - +
715A PHE* 1.3 59.5 + - - +
717A ILE* 2.8 30.9 - - - +
718A ALA* 3.7 4.2 + - - +
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Residues in contact with PHE 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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395A GLN* 3.3 21.1 - - + -
396A GLY* 4.9 6.7 - - - -
397A ASP* 5.4 4.5 - - + -
526A PRO* 3.1 35.7 - - + -
527A ILE 3.6 18.8 - - - -
528A PRO* 4.6 6.6 - - + +
544A ILE* 2.8 44.2 - - + -
545A ASP 4.2 13.0 - - - -
546A GLU* 5.2 5.4 - - - -
713A ASP* 3.4 12.1 + - - +
714A GLY* 1.3 75.5 - - - +
716A LYS* 1.3 55.0 + - + +
717A ILE 2.7 4.7 - - - -
718A ALA* 2.5 26.2 + - + +
719A GLU* 2.6 21.3 + - + +
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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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707A PHE* 3.7 11.9 - - + -
711A ASN* 5.7 3.8 - - + -
713A ASP* 4.0 33.2 + - + +
715A PHE* 1.3 76.8 - - + +
717A ILE* 1.3 56.2 + - - +
719A GLU* 3.6 17.4 - - + +
720A TYR* 3.0 26.5 + - - +
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Residues in contact with ILE 717 (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* 3.6 36.9 - - + +
672A ALA* 5.1 2.9 - - + +
675A HIS* 4.4 16.6 - - + +
678A ARG* 4.7 9.6 - - - +
707A PHE* 4.6 6.1 - - + -
708A PHE* 5.0 4.5 - - + -
711A ASN* 4.0 24.5 - - + +
713A ASP 2.7 23.6 - - - +
714A GLY* 2.8 23.3 - - - +
716A LYS* 1.3 74.6 - - - +
718A ALA* 1.3 54.8 + - - +
720A TYR* 2.6 8.3 + - - +
721A ASP* 2.4 33.4 + - - -
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Residues in contact with ALA 718 (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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526A PRO 5.3 2.7 - - - +
527A ILE* 4.6 4.7 - - - +
528A PRO* 3.2 35.9 - - + -
714A GLY 3.7 5.1 + - - +
715A PHE* 2.5 15.4 + - - +
717A ILE* 1.3 73.2 - - - +
719A GLU* 1.3 76.9 - - - +
720A TYR 2.5 1.9 + - - -
721A ASP* 2.7 17.9 + - + +
722A LEU* 2.9 11.8 + - + +
729A GLU* 5.2 6.7 - - - +
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Residues in contact with GLU 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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528A PRO* 3.1 26.7 - - + +
715A PHE* 2.6 19.3 + - + +
716A LYS* 3.6 22.7 - - + +
718A ALA* 1.3 80.2 - - - +
720A TYR* 1.3 61.7 + - - +
722A LEU* 3.2 9.3 + - - +
723A LYS* 3.1 45.9 + - + +
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Residues in contact with TYR 720 (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* 3.7 17.5 - - + -
703A GLU* 3.7 25.7 + - + +
704A ARG* 3.6 23.1 - - + +
707A PHE* 3.5 45.1 - + + -
716A LYS 3.0 19.9 + - - +
717A ILE 2.6 10.8 + - - +
718A ALA 2.5 2.2 + - - -
719A GLU* 1.3 74.5 - - - +
721A ASP* 1.3 60.2 + - - -
723A LYS* 4.3 8.5 - - + -
724A THR* 3.0 35.8 + - - +
725A ARG* 3.7 17.8 + - - -
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Residues in contact with ASP 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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670A GLY* 4.8 1.3 - - - -
671A LEU* 2.0 54.2 + - - +
672A ALA* 3.9 5.0 - - - +
717A ILE 2.4 22.0 + - - +
718A ALA* 2.7 13.2 + - - +
720A TYR* 1.3 75.0 - - - +
722A LEU* 1.3 51.7 + - - +
725A ARG* 2.5 67.2 + - - +
729A GLU* 4.2 19.0 - - - +
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Residues in contact with LEU 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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528A PRO* 4.1 23.3 - - + -
530A SER* 4.2 1.3 - - - +
531A MET* 5.0 9.2 - - + -
718A ALA* 2.9 6.8 + - - +
719A GLU* 3.3 16.2 - - - +
721A ASP* 1.3 74.7 - - - +
723A LYS* 1.3 72.9 + - + +
724A THR 3.0 11.8 + - - +
725A ARG 3.6 7.2 - - - +
726A GLY* 4.1 3.1 + - - -
727A PRO* 3.8 33.9 - - + -
729A GLU* 6.0 2.5 - - - +
741A PHE* 3.4 44.0 - - + -
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Residues in contact with LYS 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 GLU* 3.1 42.7 + - + +
720A TYR* 4.3 8.3 - - + +
722A LEU* 1.3 84.5 - - - +
724A THR* 1.3 65.6 + - - +
741A PHE* 5.6 9.7 + - - +
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Residues in contact with THR 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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700A GLU* 5.0 3.6 - - - +
703A GLU* 5.0 7.0 - - - +
704A ARG* 2.7 33.7 - - - +
720A TYR* 3.0 36.8 + - + +
722A LEU 3.1 6.8 - - - +
723A LYS* 1.3 84.9 - - - +
725A ARG* 1.3 70.6 + - - +
726A GLY 3.4 2.3 + - - -
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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