Contacts of the helix formed by residues 203 - 207 (chain B) in PDB entry 5W97
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 ASN 203 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B TRP* 3.4 48.4 - - + +
201B GLY 3.3 0.6 - - - -
202B SER* 1.3 96.5 + - - +
204B HIS* 1.3 67.3 + - - +
205B SER 3.0 2.7 - - - -
206B PHE* 2.8 46.5 + - + +
207B MET* 3.9 2.1 + - - +
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Residues in contact with HIS 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ASN* 5.3 0.7 - - - +
369A ASP* 5.1 1.6 + - - -
438A ARG 3.4 12.5 + - - -
439A ARG* 3.2 31.4 - - + +
440A TYR* 3.3 26.5 + + - -
104B TRP* 3.9 2.6 - - - -
196B CYS* 3.4 23.0 - - - +
197B SER* 4.2 2.0 - - - -
198B GLU 3.0 22.3 + - - -
199B ILE* 3.4 17.6 + - + -
200B CYS* 3.4 16.4 - - - +
201B GLY 3.2 17.6 + - - +
202B SER 3.5 0.4 - - - -
203B ASN* 1.3 77.2 - - - +
205B SER* 1.3 61.3 + - - +
206B PHE 3.2 1.2 + - - -
207B MET* 4.0 9.1 + - - +
301B CUA 2.0 32.7 - - - -
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Residues in contact with SER 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ASP* 3.8 3.1 + - - -
439A ARG 4.2 2.1 + - - -
440A TYR* 3.3 40.2 + - - -
441A SER* 3.2 29.5 + - - -
442A ASP 4.2 5.5 - - - +
135B LEU* 4.9 6.9 - - - +
195B GLN* 4.1 8.3 + - - -
202B SER 5.1 0.6 + - - -
203B ASN* 3.0 2.0 + - - +
204B HIS* 1.3 78.0 - - - +
206B PHE* 1.3 86.5 + - - +
207B MET 3.8 2.0 + - - -
208B PRO* 5.6 0.3 - - - +
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Residues in contact with PHE 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A THR* 6.2 3.4 - - - -
51A ASP* 3.5 28.0 - - - -
441A SER* 3.9 10.3 - - - -
442A ASP* 4.3 10.8 - - + -
104B TRP* 4.2 9.4 - - - +
122B MET* 3.7 35.6 + - + +
135B LEU* 3.7 37.7 - - + -
203B ASN* 2.8 41.2 + - + +
204B HIS 3.2 0.2 - - - -
205B SER* 1.3 96.2 - - - +
207B MET* 1.3 60.6 + - - +
208B PRO* 3.6 5.8 - - - -
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Residues in contact with MET 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440A TYR* 5.6 0.6 + - - -
102B HIS 3.4 23.8 - - - +
104B TRP* 3.7 22.7 - - - +
105B TYR* 3.8 14.1 - - - +
106B TRP* 3.0 49.4 + - + +
120B SER 6.1 0.2 - - - -
121B TYR* 6.5 0.2 - - - +
122B MET* 5.1 2.0 - - - +
161B HIS* 3.5 11.0 - - + +
195B GLN* 5.0 0.2 - - - -
196B CYS* 3.6 21.6 + - + -
200B CYS* 3.7 7.9 - - - -
203B ASN 3.9 9.4 - - - +
204B HIS 4.0 3.1 + - - +
205B SER 3.8 2.0 + - - -
206B PHE* 1.3 79.5 - - - +
208B PRO* 1.3 64.8 - - - +
301B CUA 2.4 29.8 - - - -
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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