Contacts of the strand formed by residues 234 - 237 (chain G) in PDB entry 5TWV
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 HIS 234 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ARG* 4.4 26.6 + - - -
255A LEU* 5.6 0.9 - - - -
258A TYR* 5.1 13.8 - + - -
219G VAL 3.1 15.6 - - - +
220G VAL* 3.5 1.6 - - - -
221G ARG 2.9 23.4 + - - +
223G THR* 3.3 32.4 + - + +
231G VAL* 3.8 21.0 + - + +
233G LEU* 1.3 72.7 - - - +
235G GLN* 1.3 78.3 + - - +
236G VAL* 4.0 16.8 + - + +
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Residues in contact with GLN 235 (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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242A ASN* 5.7 0.3 - - - +
249A ILE* 3.6 18.9 - - + +
250A PHE* 3.4 29.6 + - - +
252A VAL* 5.3 4.9 - - - +
253A ALA* 6.1 1.2 - - - +
255A LEU* 3.5 36.5 - - + +
35G PHE* 5.2 8.3 - - - -
218G GLN* 3.3 31.4 + - + +
219G VAL 3.8 2.5 - - - -
220G VAL* 4.4 20.8 - - + +
233G LEU* 3.9 5.9 + - - +
234G HIS* 1.3 85.6 + - - +
236G VAL* 1.3 60.2 + - - +
237G ASP 4.3 0.2 + - - -
284G ILE* 4.4 9.3 - - + +
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Residues in contact with VAL 236 (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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243A GLY 6.3 1.3 - - - +
218G GLN* 3.7 3.1 - - - +
219G VAL* 3.0 47.7 + - + +
234G HIS* 3.8 18.3 + - + +
235G GLN* 1.3 74.7 - - - +
237G ASP* 1.3 72.6 + - - +
238G ILE* 3.9 0.7 + - + -
264G ASN 5.8 2.2 - - - +
266G PRO* 4.1 25.4 - - + -
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Residues in contact with ASP 237 (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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242A ASN* 5.3 10.6 + - + +
243A GLY* 5.8 2.7 - - - +
244A VAL* 3.4 38.4 + - + +
246A GLY* 5.7 2.9 - - - -
216G HIS* 5.3 10.5 - - - -
217G MET 3.0 15.0 + - - +
218G GLN* 3.6 22.6 - - - +
236G VAL* 1.3 84.6 - - - +
238G ILE* 1.3 93.7 + - - +
239G PRO* 4.3 1.7 - - - +
240G MET* 5.8 0.3 - - - +
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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