Contacts of the strand formed by residues 228 - 235 (chain C) in PDB entry 4TZQ
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 GLN 228 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226C ASP 4.1 9.7 + - - +
227C ILE* 1.3 84.3 + - - +
229C SER* 1.3 63.1 + - - +
247C TRP* 3.2 6.1 - - - +
248C SER 2.9 40.2 + - - +
249C MET* 5.9 1.6 - - - -
251C MET* 3.6 29.1 - - + +
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Residues in contact with SER 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C GLN* 1.3 77.3 - - - +
230C ALA* 1.3 65.5 + - - +
245C GLU* 5.7 3.8 - - - -
246C CYS 3.2 7.4 - - - -
247C TRP* 3.5 35.1 - - - -
251C MET* 3.7 7.4 - - - +
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Residues in contact with ALA 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C LEU* 4.0 26.9 - - + -
185C VAL* 6.0 0.2 - - + -
229C SER* 1.3 78.0 - - - +
231C THR* 1.3 65.7 + - - +
232C ILE* 3.3 2.9 + - - +
245C GLU* 4.7 2.5 - - - -
246C CYS* 3.0 31.6 + - - +
251C MET* 4.0 15.3 - - + -
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Residues in contact with THR 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C LYS* 4.0 24.7 + - - +
177C SER* 5.0 2.6 + - - -
181C LEU* 5.5 1.4 - - - +
230C ALA* 1.3 71.9 - - - +
232C ILE* 1.3 63.2 + - - +
233C GLY* 3.7 15.9 - - - +
234C HIS* 6.1 0.2 - - - +
243C ASN* 4.1 7.0 + - - +
244C MET 4.1 3.1 - - - +
245C GLU* 4.4 15.5 + - - +
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Residues in contact with ILE 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C PHE* 3.9 22.0 - - + -
173C THR* 4.2 4.2 - - - +
174C ILE* 3.5 38.4 - - + +
177C SER* 3.0 32.8 + - - -
178C VAL* 3.8 14.1 - - + +
181C LEU* 4.1 14.8 - - + -
230C ALA 3.9 2.2 - - - +
231C THR* 1.3 74.7 - - - +
233C GLY* 1.3 57.5 + - - +
244C MET* 2.8 48.2 + - + +
245C GLU 3.9 2.2 - - - -
246C CYS* 3.8 19.7 - - + +
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Residues in contact with GLY 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C THR* 5.0 7.9 - - - -
174C ILE* 3.8 13.9 - - - +
231C THR* 3.6 9.6 - - - +
232C ILE* 1.3 81.4 - - - +
234C HIS* 1.3 62.7 + - - -
243C ASN* 4.0 4.3 - - - -
244C MET* 2.8 31.3 + - - +
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Residues in contact with HIS 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C LYS* 4.1 19.7 + - - -
156C LEU* 4.5 0.7 - - + -
159C LEU* 3.5 42.4 - - + +
170C GLN* 3.2 50.3 + - + +
174C ILE* 4.2 1.8 - - - +
233C GLY* 1.3 76.0 - - - +
235C LEU* 1.3 69.5 + - - +
236C ARG 4.7 0.2 - - - -
242C ALA 3.1 14.4 - - - +
243C ASN* 3.8 11.7 - - - +
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Residues in contact with LEU 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C PHE* 4.1 18.8 - - + -
42C MET* 3.7 32.1 - - + -
45C ALA* 3.8 19.1 - - + +
127C MET* 4.1 13.7 - - + -
159C LEU* 5.0 1.0 - - - +
170C GLN* 3.4 4.9 - - + +
171C MET* 4.1 23.6 - - + +
174C ILE* 3.6 29.4 - - + -
234C HIS* 1.3 80.7 - - - +
236C ARG* 1.3 62.1 + - - +
237C PRO* 3.6 4.0 - - + -
241C ALA* 3.3 7.8 - - - +
242C ALA* 2.8 41.0 + - + +
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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