Contacts of the helix formed by residues 628 - 636 (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 LYS 628 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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619A MET* 4.2 33.7 - - + +
621A GLY* 4.0 26.5 + - - +
622A ARG* 4.4 14.5 - - - +
624A SER* 4.4 11.1 - - - -
625A GLN 3.5 15.0 - - - +
626A GLU* 3.0 13.9 + - + +
627A GLU* 1.3 74.8 - - - +
629A ASP* 1.3 62.4 + - - +
630A ARG 3.1 1.3 - - - -
631A VAL* 2.5 39.7 + - - +
632A MET* 3.1 7.3 + - + +
647A THR* 4.3 14.4 + - - -
650A GLU* 2.8 33.2 + - + +
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Residues in contact with ASP 629 (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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426A THR* 2.6 38.2 - - - +
428A ILE* 4.3 12.3 - - + -
429A LEU* 4.1 2.3 - - - +
626A GLU* 3.4 11.8 - - - +
628A LYS* 1.3 79.9 + - - +
630A ARG* 1.3 75.2 - - - +
631A VAL 2.6 2.8 + - - -
632A MET* 2.7 20.6 + - - +
633A LEU* 2.7 13.2 + - - +
652A GLY* 5.8 0.7 - - - -
653A ILE* 3.5 27.2 - - + +
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Residues in contact with ARG 630 (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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428A ILE* 1.5 54.4 - - - +
627A GLU* 3.4 46.8 + - + +
629A ASP* 1.3 84.6 - - - +
631A VAL* 1.3 53.2 + - + +
633A LEU* 3.5 12.3 - - - +
634A GLU* 2.7 46.4 + - - +
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Residues in contact with VAL 631 (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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618A LEU 5.6 1.8 - - - +
619A MET* 4.4 30.1 - - + +
627A GLU 4.6 6.3 - - - +
628A LYS* 2.5 23.7 + - - +
630A ARG* 1.3 70.6 - - + +
632A MET* 1.3 58.5 + - + +
634A GLU* 3.0 17.2 + - - +
635A PHE* 2.7 23.4 + - + +
640A TYR* 3.5 27.5 - - + +
643A LEU* 4.7 10.3 - - + -
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Residues in contact with MET 632 (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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582A PHE* 3.4 37.0 - - + -
619A MET* 4.9 11.0 - - + -
628A LYS 3.1 8.7 + - - +
629A ASP* 2.7 12.8 + - - +
631A VAL* 1.3 69.7 - - + +
633A LEU* 1.3 69.1 + - - +
635A PHE* 2.4 21.9 + - + +
636A ALA* 2.5 11.4 + - - +
643A LEU* 4.4 8.1 - - + -
649A ILE* 3.6 26.7 - - + -
650A GLU 5.5 3.1 - - - +
653A ILE* 2.9 42.2 - - + +
655A VAL* 4.3 9.2 - - + -
680A ARG* 4.5 8.3 - - - -
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Residues in contact with LEU 633 (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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428A ILE* 3.3 33.0 - - + +
432A GLN* 4.1 20.4 - - + +
629A ASP 2.7 13.6 + - - +
630A ARG* 3.5 16.8 - - - +
632A MET* 1.3 74.0 - - - +
634A GLU* 1.3 57.0 + - + +
636A ALA* 2.6 22.3 + - + +
637A GLU* 3.1 42.9 - - + +
653A ILE* 2.3 28.2 - - + +
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Residues in contact with GLU 634 (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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630A ARG* 2.7 42.5 - - - +
631A VAL* 3.2 25.5 + - - +
632A MET 2.8 0.6 + - - -
633A LEU* 1.3 75.6 - - + +
635A PHE* 1.3 58.3 + - - +
637A GLU* 4.2 11.2 - - - +
638A GLY 3.5 2.6 + - - -
639A ARG* 2.9 58.3 + - - +
640A TYR* 3.9 24.9 + - + -
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Residues in contact with PHE 635 (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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580A GLN* 3.5 32.6 + - + +
581A ALA 4.3 7.4 - - - -
582A PHE* 3.9 10.1 - + - -
631A VAL 2.7 11.5 + - - +
632A MET* 2.4 21.8 + - + +
634A GLU* 1.3 70.8 - - - +
636A ALA* 1.3 55.0 + - - -
637A GLU 2.9 7.2 + - - -
638A GLY* 3.3 9.5 + - - -
639A ARG 4.0 0.2 + - - -
640A TYR* 2.7 44.0 - - + +
641A ASP 3.9 3.8 - - - -
642A ILE* 3.3 13.9 - - - -
643A LEU* 2.9 43.5 - - + -
655A VAL* 3.3 47.1 - - + -
658A ALA* 4.8 0.2 - - + -
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Residues in contact with ALA 636 (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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432A GLN* 6.1 2.5 - - - +
580A GLN* 4.6 4.3 - - - -
632A MET 2.5 16.2 + - - +
633A LEU* 2.6 11.7 + - + +
635A PHE* 1.3 68.9 - - - +
637A GLU* 1.3 61.3 + - - +
638A GLY* 4.5 0.2 - - - -
653A ILE* 5.1 3.4 - - + -
654A ASP 4.0 4.7 - - - +
655A VAL* 3.6 33.4 - - + +
656A PRO* 3.7 17.3 - - + +
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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