Contacts of the helix formed by residues 699 - 708 (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 GLY 699 (chain M).
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Specific contacts
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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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Residues in contact with VAL 700 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91M MET* 5.8 0.9 - - + -
102M VAL* 4.6 8.5 - - + -
106M LEU* 6.1 1.1 - - + -
119M SER* 3.9 15.3 - - - +
122M PHE* 3.4 31.1 - - + -
124M VAL* 4.2 21.3 - - + -
673M ARG* 4.7 4.7 - - + -
675M ILE* 5.7 0.2 - - + -
695M LEU* 3.7 19.1 - - + +
698M ASN* 3.4 19.9 - - + +
699M GLY* 1.3 77.2 - - - +
701M LEU* 1.3 79.5 + - + +
703M GLY* 3.2 1.2 + - - -
704M ILE* 3.2 25.7 + - + +
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Residues in contact with LEU 701 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98M HIS 5.2 2.5 - - - +
99M GLU* 3.6 37.5 - - + +
102M VAL* 4.4 17.3 - - + -
692M LEU* 4.6 2.5 - - + +
695M LEU* 3.0 43.4 + - + +
696M ARG* 4.0 21.3 - - + +
700M VAL* 1.3 94.3 - - + +
702M GLU* 1.3 61.1 + - - +
704M ILE* 3.9 11.9 - - + +
705M ARG* 3.2 43.0 + - - +
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Residues in contact with GLU 702 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488M GLN* 4.9 10.4 - - - +
491M PHE* 5.4 0.4 - - - -
492M ASN* 3.7 20.1 + - - -
518M ASP* 5.9 1.2 - - - +
519M LEU* 4.8 4.2 - - - +
584M TYR* 4.4 27.5 - - + +
695M LEU 4.9 0.2 + - - -
696M ARG 5.4 5.3 + - - +
699M GLY* 2.9 15.6 + - - +
701M LEU* 1.3 79.1 - - - +
703M GLY* 1.3 63.6 + - - +
704M ILE 3.2 0.2 - - - -
705M ARG* 3.5 17.6 - - - +
706M ILE* 3.1 46.9 + - + +
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Residues in contact with GLY 703 (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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119M SER 5.7 0.9 - - - -
122M PHE* 4.8 3.4 - - - -
491M PHE* 4.3 20.6 - - - -
495M MET* 4.3 6.7 - - - +
699M GLY 2.8 13.6 + - - -
700M VAL 3.2 2.6 + - - -
702M GLU* 1.3 78.7 - - - +
704M ILE* 1.3 68.0 + - - +
706M ILE* 3.8 6.3 + - - +
707M CYS* 3.1 29.3 + - - +
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Residues in contact with ILE 704 (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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91M MET 5.8 1.6 - - - +
92M ALA* 4.8 15.0 - - + +
97M LEU* 4.2 38.1 - - + +
98M HIS 4.8 6.7 - - - +
102M VAL* 4.3 19.3 - - + -
119M SER* 3.1 36.1 - - - +
700M VAL* 3.2 15.8 + - + +
701M LEU* 3.9 14.8 - - + +
702M GLU 3.2 0.2 - - - -
703M GLY* 1.3 79.6 - - - +
705M ARG* 1.3 62.5 + - - +
707M CYS* 3.0 7.4 + - + +
708M ARG* 2.9 34.9 + - - +
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Residues in contact with ARG 705 (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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99M GLU* 4.2 18.5 + - - -
696M ARG* 6.0 3.2 - - - +
701M LEU* 3.2 38.1 + - - +
702M GLU* 3.5 26.2 - - - +
704M ILE* 1.3 82.9 - - - +
706M ILE* 1.3 61.8 + - + +
708M ARG* 3.0 50.1 + - - +
709M LYS* 3.3 20.0 + - + +
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Residues in contact with ILE 706 (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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491M PHE* 5.0 1.8 - - + -
492M ASN* 4.1 25.6 - - + +
495M MET* 3.7 23.8 - - - -
499M GLU* 4.9 8.8 - - + +
515M PHE* 3.7 60.3 - - + -
702M GLU* 3.1 31.4 + - - +
703M GLY* 3.9 6.5 - - - +
705M ARG* 1.3 81.3 - - + +
707M CYS* 1.3 63.6 + - - +
709M LYS* 3.6 17.0 + - + +
710M GLY* 4.0 4.9 + - - -
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Residues in contact with CYS 707 (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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92M ALA* 4.7 19.7 - - + +
97M LEU* 4.9 9.4 - - + -
120M GLY* 5.8 1.6 - - - -
495M MET* 4.0 21.3 - - - -
499M GLU* 5.2 9.1 - - - +
703M GLY 3.1 18.4 + - - +
704M ILE* 3.0 15.5 + - + +
705M ARG 2.9 0.2 - - - -
706M ILE* 1.3 75.6 - - - +
708M ARG* 1.3 57.8 + - - +
709M LYS 2.9 10.1 + - - -
710M GLY* 3.1 12.5 + - - -
711M PHE 4.2 0.2 + - - -
712M PRO* 3.5 26.9 - - + +
714M ARG* 5.3 3.7 + - - +
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Residues in contact with ARG 708 (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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97M LEU* 2.8 54.4 + - + -
98M HIS* 4.3 8.3 - - - +
99M GLU 5.2 0.6 - - - +
704M ILE* 2.9 19.9 + - - +
705M ARG* 3.0 46.6 + - - +
707M CYS* 1.3 74.2 - - - +
709M LYS* 1.3 61.2 + - + +
710M GLY 3.5 3.9 - - - +
712M PRO* 4.1 11.3 - - + +
768M LYS* 4.8 5.0 + - - +
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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