Contacts of the helix formed by residues 672 - 680 (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 ALA 672 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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525A THR* 5.4 8.8 - - + +
670A GLY* 3.0 4.6 + - - -
671A LEU* 1.3 77.8 - - - +
673A GLN* 1.3 55.6 + - + +
674A LEU* 3.1 3.6 - - - +
675A HIS* 2.6 19.0 + - - +
676A GLN* 2.5 36.5 + - - +
717A ILE* 5.2 3.6 - - + -
721A ASP* 3.9 4.0 - - - +
729A GLU* 4.2 15.9 - - - +
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Residues in contact with GLN 673 (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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648A VAL* 2.6 44.8 - - + +
668A ARG 5.0 2.2 + - - -
669A PHE* 4.1 17.9 - - + +
670A GLY* 3.9 19.5 + - - +
672A ALA* 1.3 76.6 - - + +
674A LEU* 1.3 61.5 + - - +
676A GLN* 2.9 16.1 - - - +
677A LEU* 2.9 29.2 + - - +
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Residues in contact with LEU 674 (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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663A ILE* 3.6 41.2 - - + +
666A PRO* 4.0 11.7 - - + -
667A GLU* 4.9 2.2 - - + +
669A PHE* 3.9 18.6 - - + +
670A GLY 3.6 17.6 + - - +
671A LEU* 4.7 8.1 - - + -
672A ALA 3.1 2.4 - - - +
673A GLN* 1.3 76.7 - - - +
675A HIS* 1.3 65.6 + - - +
677A LEU* 3.1 9.0 + - - +
678A ARG* 2.8 20.8 + - - +
692A LEU* 5.2 2.2 - - + -
705A LEU* 4.0 19.1 - - + -
708A PHE* 3.4 38.2 - - + -
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Residues in contact with HIS 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A ASP* 4.3 17.4 + - - -
398A VAL* 6.5 0.2 - - + -
525A THR* 6.2 1.6 - - + -
526A PRO* 5.9 6.1 - - + -
672A ALA* 2.6 24.7 + - - +
674A LEU* 1.3 72.6 - - - +
676A GLN* 1.3 76.8 - - - +
678A ARG* 2.7 47.6 + - + +
679A GLY* 2.7 13.5 + - - -
708A PHE* 4.5 4.2 - - + -
711A ASN 5.6 0.4 - - - -
712A THR 6.5 0.2 - - - -
713A ASP 5.7 0.2 - - - -
714A GLY* 3.6 35.3 + - - -
717A ILE* 4.4 16.1 - - + +
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Residues in contact with GLN 676 (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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398A VAL* 6.0 0.2 - - - +
525A THR* 4.5 21.5 - - + +
648A VAL* 3.2 20.9 + - - +
649A ILE 2.0 37.6 + - - -
650A GLU* 3.6 14.2 - - - +
651A VAL* 5.0 16.4 - - + +
672A ALA 2.5 13.7 + - - +
673A GLN* 2.9 17.9 - - - +
675A HIS* 1.3 83.4 - - - +
677A LEU* 1.3 55.7 + - - +
679A GLY* 2.7 23.6 + - - -
680A ARG* 3.2 13.2 + - - +
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Residues in contact with LEU 677 (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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584A VAL* 4.0 17.3 - - + -
648A VAL* 3.9 13.9 - - + -
649A ILE* 3.7 32.3 - - + +
661A MET* 3.6 29.2 - - - +
663A ILE* 3.8 26.9 - - + -
669A PHE* 4.0 26.7 - - + -
673A GLN 2.9 16.3 + - - +
674A LEU* 3.2 8.7 - - - +
675A HIS 2.9 0.6 + - - -
676A GLN* 1.3 76.4 - - - +
678A ARG* 1.3 62.8 + - - +
680A ARG* 3.2 22.7 + - + +
681A VAL 4.1 0.3 + - - -
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Residues in contact with ARG 678 (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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553A GLU* 5.3 4.6 + - - -
554A VAL* 4.5 19.9 - - + +
556A THR* 3.7 24.8 + - + -
661A MET* 4.9 0.2 - - - +
663A ILE* 5.0 1.1 - - + +
674A LEU 2.8 7.1 + - - +
675A HIS* 2.7 40.5 + - + +
677A LEU* 1.3 73.9 - - - +
679A GLY* 1.3 65.2 + - - +
681A VAL* 3.3 17.5 + - - +
690A CYS* 3.2 32.0 - - - +
708A PHE* 1.3 82.0 + - + -
709A THR 5.0 1.4 + - - -
711A ASN 3.3 26.7 + - - +
712A THR* 4.9 3.6 - - - +
717A ILE* 4.7 4.0 - - - +
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Residues in contact with GLY 679 (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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398A VAL* 4.1 22.4 - - - +
554A VAL* 6.2 0.4 - - - -
675A HIS* 2.7 12.3 + - - -
676A GLN 2.7 16.1 + - - -
678A ARG* 1.3 71.9 - - - +
680A ARG* 1.3 51.7 + - - -
681A VAL 2.5 17.2 + - - -
683A ARG* 2.6 27.0 + - - -
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Residues in contact with ARG 680 (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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398A VAL* 5.0 6.3 - - - +
582A PHE* 3.4 27.5 - - + -
632A MET* 4.5 9.2 - - - -
649A ILE* 5.0 12.3 + - + +
650A GLU 3.5 22.6 + - - +
651A VAL* 2.9 43.9 + - - +
652A GLY 2.9 6.9 + - - +
653A ILE 3.8 18.8 + - - -
654A ASP* 4.5 12.6 + - - +
655A VAL* 4.9 3.3 + - - +
658A ALA* 4.4 3.1 - - - +
661A MET* 5.6 0.7 - - - -
676A GLN* 3.2 13.5 + - - +
677A LEU* 3.2 19.9 + - + +
679A GLY* 1.3 74.6 - - - +
681A VAL* 1.3 67.9 + - - +
683A ARG* 4.3 16.6 - - - +
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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