Contacts of the helix formed by residues 594 - 601 (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 594 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277M PHE* 6.4 2.5 - - - -
547M ASP* 2.9 12.9 + - - -
593M SER* 1.3 74.5 - - - +
595M TRP* 1.3 59.2 + - - +
596M LEU 3.2 2.5 - - - -
597M GLU* 3.1 12.1 + - - +
598M LYS* 2.7 44.5 + - - +
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Residues in contact with TRP 595 (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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473M ASN 4.5 2.0 - - - -
474M SER* 2.8 19.6 + - - -
475M PHE* 3.0 41.9 - + + +
478M LEU* 4.0 28.5 - - + -
532M ILE* 5.3 1.6 - - + -
536M LEU* 3.9 26.9 - - + -
547M ASP* 4.0 1.0 + - - +
550M PHE* 4.1 22.0 - + + -
579M PHE* 4.4 16.2 - + - -
590M TYR* 4.3 16.6 - - + -
591M ASN 2.8 31.8 + - - -
592M ILE* 3.5 10.1 - - + -
593M SER 3.1 16.5 - - - +
594M GLY* 1.3 82.8 - - - +
596M LEU* 1.3 55.5 + - - +
598M LYS* 3.6 7.3 - - - +
599M ASN* 2.6 41.4 + - - +
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Residues in contact with LEU 596 (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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424M ASN* 5.6 4.0 - - - +
536M LEU* 3.8 18.8 - - + -
539M GLU* 4.6 11.0 - - + +
540M CYS* 3.8 12.6 - - - -
545M ALA* 3.8 28.3 - - + +
546M THR 3.5 30.5 - - - +
547M ASP* 3.4 13.1 + - - +
550M PHE* 3.8 28.3 - - + -
594M GLY 3.2 0.6 - - - -
595M TRP* 1.3 80.2 - - - +
597M GLU* 1.3 61.7 + - - +
599M ASN* 3.6 3.5 - - - +
600M LYS* 3.2 38.7 + - - +
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Residues in contact with GLU 597 (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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276M THR* 3.1 29.4 - - - +
277M PHE* 5.8 1.6 - - - +
314M TYR* 5.4 3.6 + - - -
423M HIS* 4.3 11.1 - - - +
424M ASN* 3.5 32.1 + - - +
427M GLY* 4.6 7.3 - - - -
431M LYS* 1.7 24.6 + - - +
547M ASP* 4.9 0.2 + - - -
594M GLY* 3.1 13.3 + - - +
596M LEU* 1.3 75.2 - - - +
598M LYS* 1.3 52.5 - - - +
599M ASN 2.9 1.3 - - - -
600M LYS* 2.5 19.9 + - - +
601M ASP 3.2 5.0 + - - -
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Residues in contact with LYS 598 (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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271M GLU* 5.3 0.2 - - - -
272M LYS* 4.4 2.3 - - - +
273M SER* 2.0 59.7 - - - +
276M THR* 5.2 4.5 - - + -
277M PHE* 4.0 35.0 - - + -
431M LYS* 1.2 95.8 - - - +
474M SER* 4.2 12.7 + - - -
475M PHE* 3.9 16.4 - - + +
476M GLU* 2.7 24.5 + - - +
593M SER 5.0 7.7 + - - -
594M GLY* 2.7 23.6 + - - +
595M TRP* 3.6 6.2 - - - +
597M GLU* 1.3 65.2 + - - +
599M ASN* 1.3 54.6 + - - +
649M VAL* 3.5 4.9 - - - +
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Residues in contact with ASN 599 (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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431M LYS* 2.3 2.8 - - - +
475M PHE* 3.6 12.3 - - + -
536M LEU* 3.6 26.8 + - + +
537M GLU* 4.4 2.2 - - - +
540M CYS* 4.0 10.8 - - - -
595M TRP 2.6 20.0 + - - +
596M LEU 3.6 4.7 - - - +
598M LYS* 1.3 78.7 - - - +
600M LYS* 1.3 59.0 + - - +
648M THR* 2.8 35.9 + - - -
649M VAL* 3.2 16.9 + - - +
650M SER* 2.7 50.7 + - - -
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Residues in contact with LYS 600 (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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421M GLN* 4.5 9.7 + - - +
424M ASN* 3.0 55.9 + - + +
425M SER* 4.0 6.0 - - - +
428M ALA* 0.7 129.3 - - + +
539M GLU 5.0 0.4 - - - -
540M CYS* 3.6 39.0 + - + +
542M PHE 4.1 16.4 + - - -
543M PRO* 5.0 2.4 + - - +
545M ALA* 5.8 1.8 + - - +
596M LEU* 3.2 27.1 + - - +
597M GLU* 2.5 19.3 + - - +
599M ASN* 1.3 73.9 - - - +
601M ASP* 1.3 46.4 - - - +
602M PRO 4.8 2.7 - - - +
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Residues in contact with ASP 601 (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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275M VAL* 4.1 1.7 - - - +
276M THR* 3.3 8.0 + - - -
427M GLY* 0.7 110.9 + - - +
428M ALA* 1.8 25.8 - - - +
429M LEU 1.8 28.4 + - - -
430M ALA* 1.8 17.8 + - - +
431M LYS* 0.6 277.0 + - + +
432M ALA 2.7 1.8 - - - +
597M GLU 3.2 0.8 + - - -
600M LYS* 1.3 63.6 - - - +
649M VAL* 4.0 2.5 - - + -
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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