Contacts of the helix formed by residues 491 - 498 (chain M) in PDB entry 6G0L
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 THR 491 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432M VAL 3.7 6.1 - - - -
433M PRO* 4.2 4.0 - - + -
434M LEU* 3.5 48.9 - - + +
437M MET* 3.7 13.4 - - - +
457M MET* 5.5 0.2 - - - +
490M THR* 1.3 79.1 - - - +
492M TYR* 1.3 76.1 + - + +
493M GLU* 3.3 11.0 - - + +
494M TYR* 3.2 40.1 + - - -
495M ILE* 3.3 16.3 + - - +
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Residues in contact with TYR 492 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J G 5.1 9.6 - - - +
431M VAL* 4.4 17.5 - - + -
433M PRO* 3.8 30.5 - - + +
490M THR 4.9 0.2 - - - -
491M THR* 1.3 82.2 - - + +
493M GLU* 1.3 61.9 + - - +
495M ILE* 3.3 23.4 + - + +
496M LEU* 3.4 21.7 - - + +
512M VAL* 3.6 20.6 - - + +
513M ASP 2.8 27.2 + - - -
514M GLU* 3.6 6.3 + - + -
517M ARG* 3.8 32.8 - - + -
525M LEU* 4.5 22.2 - - + +
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Residues in contact with GLU 493 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-19I G 5.5 1.9 + - - -
-18I C 1.7 59.1 + - - +
-17I T 2.5 32.0 + - - +
20J G 6.2 0.2 - - - -
21J G 4.8 9.6 - - - +
434M LEU* 3.7 1.4 - - - +
491M THR* 4.3 10.5 - - + +
492M TYR* 1.3 76.4 - - - +
494M TYR* 1.3 70.9 + - + +
496M LEU* 3.4 3.9 + - - +
497M LYS* 2.9 33.9 + - - +
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Residues in contact with TYR 494 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-17I T 2.2 45.5 + - - -
434M LEU* 6.0 0.4 - - + -
456M TYR* 3.3 50.1 - + + -
457M MET* 3.6 12.8 - - + +
458M GLY 2.9 36.0 + - - -
459M ASN* 5.6 0.9 - - - -
490M THR* 3.7 7.6 - - + -
491M THR* 3.2 35.1 + - - +
493M GLU* 1.3 79.5 - - + +
495M ILE* 1.3 60.4 + - - +
497M LYS* 3.9 15.0 - - + -
498M ASP* 3.0 33.1 + - - +
502M LEU* 4.4 2.6 - - - +
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Residues in contact with ILE 495 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429M ILE* 5.9 1.8 - - + -
431M VAL* 3.6 29.6 - - + -
490M THR* 3.8 11.4 - - + -
491M THR 3.3 15.0 - - - +
492M TYR* 3.5 11.2 - - + +
493M GLU 3.2 1.0 - - - -
494M TYR* 1.3 77.0 - - - +
496M LEU* 1.3 64.5 + - + +
498M ASP 3.1 21.0 - - - +
499M ARG* 3.2 14.4 - - - +
502M LEU* 4.4 6.3 - - + -
525M LEU* 4.0 22.9 - - + -
528M SER* 3.3 26.7 - - - +
529M LEU* 4.1 8.5 - - + -
532M PHE* 4.1 23.1 - - + -
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Residues in contact with LEU 496 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J G 2.6 67.8 + - - -
21J G 2.8 17.9 - - - +
492M TYR* 3.4 16.8 - - + +
493M GLU* 3.4 6.8 + - - +
495M ILE* 1.3 82.7 - - + +
497M LYS* 1.3 61.4 + - - +
499M ARG* 3.0 37.0 + - - +
524M SER* 3.7 15.9 - - - +
525M LEU* 4.2 23.8 - - + -
528M SER* 5.1 2.0 - - - +
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Residues in contact with LYS 497 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-17I T 2.7 45.4 + - - -
-16I T 3.4 17.6 + - - +
20J G 5.9 0.7 - - - -
459M ASN* 5.5 3.4 - - - +
463M ARG* 6.1 0.7 - - - +
493M GLU* 2.9 20.6 + - - +
494M TYR* 4.2 15.2 - - + +
496M LEU* 1.3 79.6 - - - +
498M ASP* 1.3 76.9 + - - +
499M ARG 4.0 1.3 + - - -
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Residues in contact with ASP 498 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456M TYR* 2.4 35.0 + - + +
459M ASN 5.7 0.3 - - - +
463M ARG* 4.0 24.5 + - - -
494M TYR* 3.0 16.1 + - - +
495M ILE* 3.1 10.7 - - - +
497M LYS* 1.3 98.8 - - - +
499M ARG* 1.3 60.5 + - - +
500M ALA 3.6 1.1 - - - -
501M GLU* 3.4 26.4 - - + +
502M LEU* 3.8 22.1 - - + +
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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