Contacts of the helix formed by residues 688 - 702 (chain M) in PDB entry 6M6A
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 PRO 688 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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686M GLN 4.9 0.7 - - - +
687M MET* 1.3 91.8 - - + +
689M GLU* 1.3 63.7 + - - +
690M SER* 3.2 10.3 - - - +
691M LEU* 3.1 48.3 + - + +
692M ILE* 3.7 1.6 + - - +
4N T 6.0 3.1 - - - +
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Residues in contact with GLU 689 (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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686M GLN 5.8 0.3 + - - -
687M MET 3.0 19.8 + - - +
688M PRO* 1.3 73.0 - - - +
690M SER* 1.3 60.0 + - - +
691M LEU 3.2 0.2 - - - -
692M ILE* 3.1 20.8 + - + +
693M GLU* 3.0 30.8 + - - +
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Residues in contact with SER 690 (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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688M PRO* 4.4 7.0 - - - +
689M GLU* 1.3 76.5 - - - +
691M LEU* 1.3 72.8 + - - +
693M GLU* 2.9 21.7 - - - +
694M GLU* 2.9 33.7 + - - +
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Residues in contact with LEU 691 (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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687M MET* 4.6 22.0 - - + -
688M PRO* 3.1 33.7 + - + +
690M SER* 1.3 92.2 + - - +
692M ILE* 1.3 60.0 + - + +
694M GLU* 3.7 13.0 - - - +
695M THR* 2.9 35.5 + - + +
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Residues in contact with ILE 692 (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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683M VAL* 4.4 18.2 - - + -
684M HIS 5.0 3.4 - - - +
685M GLY* 5.1 4.5 - - - -
687M MET* 4.2 22.9 - - + -
688M PRO 3.9 3.1 - - - +
689M GLU* 3.1 36.3 + - + +
691M LEU* 1.3 77.5 - - + +
693M GLU* 1.3 58.3 + - - +
695M THR* 2.3 23.9 + - - +
696M MET* 3.0 31.8 + - + +
714M GLU* 4.4 17.0 - - - +
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Residues in contact with GLU 693 (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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689M GLU 3.0 16.7 + - - +
690M SER* 2.9 30.3 - - - +
692M ILE* 1.3 77.4 - - - +
694M GLU* 1.3 62.5 + - - +
696M MET* 3.2 12.8 + - + +
697M LEU* 2.9 49.8 + - + +
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Residues in contact with GLU 694 (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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690M SER* 2.9 25.1 + - - +
691M LEU* 3.7 15.0 - - - +
692M ILE 3.2 0.2 - - - -
693M GLU* 1.3 80.6 - - - +
695M THR* 1.3 56.3 + - + +
697M LEU* 3.4 22.1 - - + +
698M LEU* 2.8 43.2 + - + +
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Residues in contact with THR 695 (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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681M GLY* 5.8 4.3 - - - -
682M VAL 5.0 8.5 - - - +
683M VAL* 4.6 22.7 - - + +
691M LEU* 2.9 18.8 + - + +
692M ILE* 2.3 31.4 + - + +
694M GLU* 1.3 73.8 - - + +
696M MET* 1.3 72.1 + - - +
698M LEU* 3.6 12.0 - - + +
699M PHE* 2.9 43.3 + - + -
704M TYR* 6.0 3.4 - - + -
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Residues in contact with MET 696 (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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683M VAL* 4.6 14.8 - - + -
692M ILE* 3.0 41.4 + - + +
693M GLU* 3.2 15.5 + - + +
695M THR* 1.3 93.3 + - - +
697M LEU* 1.3 56.8 + - - +
699M PHE* 3.4 4.4 + - + +
700M ALA* 2.9 25.3 + - - +
707M LEU* 5.5 14.1 - - + -
714M GLU* 5.2 8.1 - - - +
717M LEU* 4.4 25.1 - - + -
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Residues in contact with LEU 697 (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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693M GLU* 2.9 39.7 + - - +
694M GLU* 3.4 23.6 - - + +
696M MET* 1.3 75.4 - - - +
698M LEU* 1.3 63.7 + - + +
699M PHE 3.4 0.2 - - - -
700M ALA* 3.6 11.2 - - + +
701M GLU* 2.8 29.0 + - + +
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Residues in contact with LEU 698 (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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694M GLU* 2.8 32.3 + - + +
695M THR* 3.2 12.7 + - + +
697M LEU* 1.3 83.1 - - + +
699M PHE* 1.3 55.4 + - + +
700M ALA 3.3 0.7 - - - -
701M GLU* 3.6 16.9 - - + +
702M GLY* 2.7 27.4 + - - -
703M ALA* 3.9 1.7 + - + -
704M TYR* 3.6 55.5 + - + +
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Residues in contact with PHE 699 (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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653M LYS* 3.3 29.6 + - + +
681M GLY* 4.6 4.0 - - - -
683M VAL* 5.2 8.1 - - + -
695M THR* 2.9 39.1 + - + +
696M MET* 3.7 4.9 - - + +
698M LEU* 1.3 73.5 - - - +
700M ALA* 1.3 60.1 + - - +
702M GLY* 3.7 3.1 - - - +
704M TYR* 3.2 37.2 - + + -
705M ASP 3.3 34.5 - - - -
706M VAL 3.2 25.8 - - - -
707M LEU* 3.5 44.2 - - + -
708M LEU 5.3 0.2 - - - -
719M VAL* 5.0 12.8 - - + +
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Residues in contact with ALA 700 (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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653M LYS* 4.7 4.9 + - - -
696M MET 2.9 17.6 + - - +
697M LEU* 3.6 12.8 - - + +
698M LEU 3.3 0.2 - - - -
699M PHE* 1.3 76.9 - - - +
701M GLU* 1.3 62.4 + - - +
702M GLY* 3.4 1.4 + - - -
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Residues in contact with GLU 701 (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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697M LEU* 2.8 21.9 + - + +
698M LEU* 4.0 15.4 - - + +
700M ALA* 1.3 71.6 - - - +
702M GLY* 1.3 56.2 + - - +
703M ALA* 3.0 36.5 + - - +
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Residues in contact with GLY 702 (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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653M LYS* 3.9 25.6 - - - -
679M ARG* 5.2 0.2 + - - -
698M LEU 2.7 17.9 + - - -
699M PHE 3.9 1.6 - - - -
700M ALA 3.1 2.9 - - - -
701M GLU* 1.3 71.8 - - - +
703M ALA* 1.3 57.9 + - - -
704M TYR 2.9 9.9 - - - +
705M ASP* 2.9 19.1 - - - +
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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