Contacts of the helix formed by residues 687 - 699 (chain G) in PDB entry 1MVW
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 GLU 687 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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677G PRO 2.8 11.4 + - - +
678G ASN* 4.1 16.3 - - + +
679G GLU* 3.8 27.7 + - - +
680G THR* 4.7 9.2 + - - +
686G MET* 1.3 73.0 - - - +
688G HIS* 1.3 67.1 + - - +
689G GLU* 4.9 3.0 - - - +
690G LEU* 4.0 23.1 + - + +
691G VAL* 3.0 23.4 + - - +
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Residues in contact with HIS 688 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G GLN* 4.4 18.6 - - + +
46G SER* 3.8 29.4 + - - +
47G PHE 4.1 8.6 + - - -
48G VAL* 6.0 0.2 - - + -
103G LEU* 4.0 22.0 - - + +
104G TYR* 3.6 25.3 - + - -
107G MLY 2.9 47.3 + - + +
686G MET* 3.8 11.7 - - + -
687G GLU* 1.3 69.7 - - - +
689G GLU* 1.3 60.9 - - - +
690G LEU 2.8 11.3 + - - -
691G VAL* 2.8 14.9 + - - +
692G LEU* 2.8 15.3 + - - +
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Residues in contact with GLU 689 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G SER* 3.5 17.9 - - - +
687G GLU* 4.9 3.2 - - - +
688G HIS* 1.3 79.2 - - - +
690G LEU* 1.3 63.2 + - - +
692G LEU* 3.7 10.9 - - + +
693G HIS* 3.1 41.4 + - + +
696G ARG* 5.7 2.5 - - - +
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Residues in contact with LEU 690 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180G GLU* 5.5 1.6 - - - +
239G ARG* 4.6 11.7 - - - +
676G ILE* 3.0 23.1 - - + +
677G PRO 3.0 32.5 - - - +
678G ASN* 3.9 8.3 - - - -
679G GLU* 3.8 30.7 - - + +
687G GLU* 4.0 23.1 - - + +
688G HIS 2.8 1.4 + - - -
689G GLU* 1.3 85.0 + - - +
691G VAL* 1.3 50.5 + - - +
693G HIS* 3.4 11.3 - - - +
694G GLN* 2.8 37.7 + - - +
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Residues in contact with VAL 691 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103G LEU* 4.5 9.9 - - + -
106G LEU* 4.6 9.0 - - + -
675G ILE* 4.3 17.3 - - + -
676G ILE 4.3 7.6 - - - +
677G PRO* 3.9 12.6 - - + +
686G MET* 3.4 36.3 - - + -
687G GLU 3.0 18.2 - - - +
688G HIS 2.8 7.4 + - - +
690G LEU* 1.3 69.6 - - - +
692G LEU* 1.3 67.0 + - - +
694G GLN* 3.1 8.0 + - - +
695G LEU* 2.9 43.3 + - + +
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Residues in contact with LEU 692 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G SER* 3.6 34.8 - - - +
47G PHE* 4.1 13.7 - - + -
99G GLU* 4.2 28.7 - - + +
103G LEU* 3.7 36.8 - - + +
688G HIS 2.8 9.5 + - - +
689G GLU* 3.7 9.9 - - + +
691G VAL* 1.3 77.3 - - - +
693G HIS* 1.3 64.3 + - - +
695G LEU* 3.1 20.6 + - + +
696G ARG* 3.0 36.4 + - - +
701G LEU* 4.8 0.9 - - + -
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Residues in contact with HIS 693 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180G GLU* 5.0 9.0 - - - +
469G ILE* 5.1 12.4 - - + +
689G GLU* 3.1 37.9 + - + +
690G LEU* 3.4 13.2 - - - +
692G LEU* 1.3 76.2 - - - +
694G GLN* 1.3 67.7 + - + +
696G ARG* 2.8 35.1 + - - +
697G CYS* 3.2 27.0 + - - -
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Residues in contact with GLN 694 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180G GLU* 4.0 26.6 + - + +
183G ALA* 5.2 0.2 - - - +
674G CYS 4.6 2.3 - - - +
675G ILE* 4.1 15.5 - - + +
676G ILE* 2.7 58.9 + - - +
690G LEU* 2.8 34.6 + - - +
691G VAL* 3.4 11.0 - - - +
693G HIS* 1.3 73.9 - - + +
695G LEU* 1.3 54.4 + - - +
696G ARG 3.0 0.3 + - - -
697G CYS* 3.2 5.9 + - - +
698G ASN* 2.6 50.1 + - - +
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Residues in contact with LEU 695 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G GLU 5.4 0.2 - - - +
102G VAL* 3.8 27.1 - - + -
103G LEU* 4.7 7.4 - - + +
106G LEU* 4.4 13.5 - - + -
675G ILE* 4.7 7.0 - - + -
691G VAL* 2.9 42.2 + - + +
692G LEU* 3.2 26.5 - - + +
694G GLN* 1.3 80.3 - - + +
696G ARG* 1.3 60.1 + - - +
698G ASN* 3.3 21.6 - - - +
700G VAL* 3.5 15.7 + - + -
701G LEU* 3.0 40.4 + - + -
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Residues in contact with ARG 696 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G PHE* 5.2 0.8 - - - -
99G GLU* 2.3 44.0 + - - -
584G TYR* 3.8 15.4 - - - -
585G ALA* 4.4 14.4 - - - +
689G GLU* 5.7 2.6 - - - +
692G LEU* 3.0 43.9 + - - +
693G HIS* 2.8 26.9 + - - +
695G LEU* 1.3 71.7 - - - +
697G CYS* 1.3 65.5 + - - +
698G ASN 3.1 4.8 + - - -
699G GLY* 3.9 6.6 + - - -
701G LEU* 4.0 17.8 - - + +
702G GLU* 5.4 4.7 + - - +
705G ARG* 6.0 2.6 - - - +
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Residues in contact with CYS 697 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180G GLU* 5.9 2.5 - - - +
466G GLY* 5.7 1.4 - - - -
467G PHE* 3.7 32.0 + - + +
468G GLU* 5.8 0.2 - - - -
469G ILE* 4.1 21.5 - - - -
484G ASN* 6.0 0.3 - - - -
584G TYR* 3.2 18.3 + - - -
585G ALA* 3.9 27.4 - - + -
693G HIS* 3.2 26.0 + - - +
694G GLN* 3.2 6.0 + - - +
696G ARG* 1.3 81.6 - - - +
698G ASN* 1.3 63.2 + - - +
699G GLY 3.4 0.2 - - - -
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Residues in contact with ASN 698 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122G PHE* 4.7 0.9 - - - -
178G THR* 4.8 11.0 + - - +
179G GLY* 5.4 2.8 - - - -
488G GLN* 3.9 4.4 - - - +
584G TYR* 5.0 0.4 + - - -
673G ARG* 3.2 54.1 + - + +
674G CYS 4.8 5.9 + - - -
675G ILE* 3.7 21.3 - - - +
694G GLN* 2.6 32.3 + - - +
695G LEU* 3.3 16.2 - - - +
697G CYS* 1.3 78.5 - - - +
699G GLY* 1.3 58.0 + - - +
700G VAL* 3.4 20.0 + - + +
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Residues in contact with GLY 699 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122G PHE* 3.5 14.4 - - - -
488G GLN* 3.5 24.2 - - - -
491G PHE* 4.7 1.7 - - - -
584G TYR* 5.4 1.6 - - - -
695G LEU 3.8 2.0 + - - -
696G ARG 3.9 5.9 + - - -
697G CYS 3.4 1.8 - - - -
698G ASN* 1.3 77.6 - - - +
700G VAL* 1.3 57.6 + - - +
701G LEU 3.2 2.2 - - - -
702G GLU* 2.9 9.4 + - - +
703G GLY* 2.8 26.5 + - - -
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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