Contacts of the helix formed by residues 687 - 699 (chain M) in PDB entry 2W4G
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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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677M PRO 2.8 11.7 + - - +
678M ASN* 4.1 16.9 - - + +
679M GLU* 3.8 26.7 + - - +
680M THR* 4.7 8.8 + - - +
686M MET* 1.3 74.0 - - - +
688M HIS* 1.3 67.2 + - - +
689M GLU* 4.9 3.0 - - - +
690M LEU* 4.0 21.4 - - + +
691M VAL* 3.0 24.3 + - - +
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Residues in contact with HIS 688 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45M GLU* 4.4 22.4 - - + +
46M SER* 3.8 28.8 + - - +
47M PHE 4.1 8.8 + - - -
103M LEU* 4.0 22.9 - - + +
104M TYR* 3.6 25.3 - + - -
107M LYS* 2.9 40.5 + - + +
686M MET* 3.8 12.7 + - + -
687M GLU* 1.3 70.0 - - - +
689M GLU* 1.3 62.5 + - - +
690M LEU 2.8 10.8 + - - -
691M VAL* 2.8 15.1 + - - +
692M LEU* 2.8 15.7 + - - +
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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
----------------------------------------------------------
46M SER* 3.5 18.4 - - - +
687M GLU* 4.9 3.7 - - - +
688M HIS* 1.3 79.0 - - - +
690M LEU* 1.3 64.5 + - - +
692M LEU* 3.7 11.2 - - + +
693M HIS* 3.1 40.4 + - + +
696M ARG* 5.7 2.5 - - - +
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Residues in contact with LEU 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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180M GLU* 5.4 5.8 - - - +
676M ILE* 3.0 26.5 - - + +
677M PRO 3.0 32.1 - - - +
678M ASN* 3.9 8.3 - - - -
679M GLU* 3.8 31.0 - - + +
687M GLU* 4.0 23.8 + - + +
688M HIS 2.8 2.0 + - - -
689M GLU* 1.3 84.5 + - - +
691M VAL* 1.3 51.1 + - - +
693M HIS* 3.4 11.3 - - - +
694M GLN* 2.8 37.7 + - - +
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Residues in contact with VAL 691 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103M LEU* 4.5 9.2 - - + -
106M LEU* 4.6 9.0 - - + -
675M ILE* 4.3 17.5 - - + -
676M ILE 4.3 4.9 - - - +
677M PRO* 3.9 13.7 - - + +
686M MET* 3.4 35.9 - - + -
687M GLU 3.0 17.7 - - - +
688M HIS 2.8 7.4 + - - +
690M LEU* 1.3 72.6 - - + +
692M LEU* 1.3 67.7 + - - +
694M GLN* 3.1 8.7 + - - +
695M LEU* 2.9 44.0 + - + +
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Residues in contact with LEU 692 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46M SER* 3.6 34.1 - - - +
47M PHE* 4.1 14.1 - - + -
99M GLU* 4.2 28.9 - - + +
103M LEU* 3.6 35.2 - - + -
688M HIS 2.8 9.2 + - - +
689M GLU* 3.7 10.1 - - + +
691M VAL* 1.3 76.8 - - - +
693M HIS* 1.3 65.3 + - - +
695M LEU* 3.1 21.9 + - + +
696M ARG* 3.0 36.1 + - - +
701M LEU* 4.8 1.1 - - + -
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Residues in contact with HIS 693 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180M GLU* 5.0 8.3 - - - +
469M ILE* 5.1 12.5 - - + +
689M GLU* 3.1 37.4 + - + +
690M LEU* 3.4 14.3 - - - +
692M LEU* 1.3 77.2 - - - +
694M GLN* 1.3 67.1 + - + +
696M ARG* 2.8 34.3 + - - +
697M CYS* 3.2 28.4 + - - -
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Residues in contact with GLN 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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180M GLU* 4.0 26.5 + - + +
674M CYS 4.6 2.8 - - - +
675M ILE* 4.1 14.8 - - + -
676M ILE* 2.7 58.3 + - - +
690M LEU* 2.8 33.7 + - - +
691M VAL* 3.5 10.9 - - - +
693M HIS* 1.3 75.3 - - + +
695M LEU* 1.3 54.5 + - - +
697M CYS* 3.2 5.7 + - - +
698M ASN* 2.6 49.9 + - - +
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Residues in contact with LEU 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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102M VAL* 3.8 27.1 - - + -
103M LEU* 4.7 7.4 - - + +
106M LEU* 4.4 14.1 - - + -
675M ILE* 4.7 6.7 - - + -
691M VAL* 2.9 41.7 + - + +
692M LEU* 3.2 26.7 - - + +
693M HIS 3.0 0.2 - - - -
694M GLN* 1.3 80.2 - - + +
696M ARG* 1.3 60.0 + - - +
698M ASN* 3.3 21.4 - - - +
700M VAL* 3.5 16.3 + - + -
701M LEU* 3.0 41.5 + - + -
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Residues in contact with ARG 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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47M PHE* 5.2 0.8 - - - -
99M GLU* 2.3 42.8 + - - -
584M TYR* 3.8 15.1 - - - -
585M ALA* 4.4 13.0 - - - +
689M GLU* 5.7 2.4 - - - +
692M LEU* 3.0 44.9 + - - +
693M HIS* 2.8 26.1 + - + +
695M LEU* 1.3 71.4 - - - +
697M CYS* 1.3 65.9 + - - +
698M ASN 3.1 4.8 + - - -
699M GLY* 3.9 6.1 + - - -
701M LEU* 4.0 16.9 - - + +
702M GLU* 5.4 5.4 + - - +
705M ARG* 6.0 2.4 - - - +
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Residues in contact with CYS 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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178M THR* 5.8 1.6 - - - +
180M GLU* 5.9 2.5 - - - +
466M GLY* 5.7 1.4 - - - -
467M PHE* 3.7 32.5 + - + +
468M GLU* 5.8 0.4 - - - -
469M ILE* 4.1 20.9 - - - -
484M ASN* 6.0 0.3 - - - -
584M TYR* 3.2 17.9 + - - -
585M ALA* 3.9 27.4 - - + -
693M HIS* 3.2 25.7 + - - +
694M GLN* 3.2 6.4 + - - +
696M ARG* 1.3 82.1 - - - +
698M ASN* 1.3 62.6 + - - +
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Residues in contact with ASN 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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122M PHE* 4.7 0.5 - - - -
178M THR* 4.8 11.8 + - - +
179M GLY* 5.4 2.8 - - - -
488M GLN* 3.9 4.3 - - - +
584M TYR* 5.0 0.2 - - - -
673M ARG* 3.2 54.9 + - + +
674M CYS 4.8 6.1 + - - -
675M ILE* 3.7 21.7 - - - +
694M GLN* 2.6 32.6 + - - +
695M LEU* 3.3 16.8 + - - +
697M CYS* 1.3 77.6 - - - +
699M GLY* 1.3 58.2 + - - +
700M VAL* 3.4 19.6 - - + +
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Residues in contact with GLY 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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122M PHE* 3.5 14.5 - - - -
488M GLN* 3.5 24.0 - - - -
491M PHE* 4.7 1.7 - - - -
584M TYR* 5.4 1.1 - - - -
695M LEU 3.8 1.6 + - - -
696M ARG 3.9 6.1 + - - -
697M CYS 3.5 2.2 - - - -
698M ASN* 1.3 78.2 - - - +
700M VAL* 1.3 56.7 + - - +
701M LEU 3.2 2.7 - - - -
702M GLU* 2.9 9.8 + - - +
703M GLY* 2.8 26.7 + - - -
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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