Contacts of the strand formed by residues 229 - 234 (chain C) in PDB entry 2VZE
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 LYS 229 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C MET* 5.8 2.0 - - - -
220C PHE* 3.2 4.7 - - - -
221C THR* 2.9 35.2 + - + +
222C SER 4.9 0.4 - - - -
223C GLY* 3.5 29.5 - - - -
224C THR* 4.8 1.4 - - - +
225C SER 4.9 6.3 + - - -
227C LEU 4.3 5.6 + - - +
228C PRO* 1.3 75.9 - - + +
230C MET* 1.3 63.1 + - - +
231C ALA 3.6 1.3 + - - -
426C TYR* 3.7 47.7 + - + -
429C ASN* 5.6 4.3 - - + +
432C LYS* 3.9 37.4 - - + +
472C ARG* 5.9 1.4 - - - +
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Residues in contact with MET 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C ARG* 4.9 0.4 - - - -
151C MET* 3.6 48.4 - - + +
152C SER* 3.8 17.9 - - - -
218C ILE* 3.6 22.4 - - + -
219C TYR 4.0 0.9 - - - -
220C PHE* 3.5 29.6 - - + +
229C LYS* 1.3 71.1 - - - +
231C ALA* 1.3 61.3 + - - +
232C GLU 3.5 0.6 + - - -
426C TYR* 3.2 7.9 - - - +
427C VAL* 2.8 73.4 + - + +
428C ASP* 4.0 7.2 - - + +
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Residues in contact with ALA 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C ALA 3.8 0.2 - - - +
218C ILE* 3.3 3.1 - - - -
219C TYR* 2.8 46.7 + - - +
221C THR* 4.2 13.5 - - + -
229C LYS 3.6 1.2 + - - -
230C MET* 1.3 69.4 - - - +
232C GLU* 1.3 61.7 + - - +
233C HIS* 3.8 5.1 + - + -
364C THR* 4.0 21.5 - - + +
365C GLU* 4.8 2.7 - - + -
423C PHE* 3.8 26.0 - - + -
426C TYR* 4.2 1.6 - - + -
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Residues in contact with GLU 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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108C ARG* 5.3 3.8 + - - -
213C GLN 4.9 3.1 - - - +
215C ALA* 3.4 35.8 + - + +
217C ALA 3.4 8.3 - - - +
218C ILE* 4.4 5.1 - - + +
230C MET 3.5 1.0 + - - -
231C ALA* 1.3 71.8 - - - +
233C HIS* 1.3 63.8 + - - +
423C PHE* 3.2 6.4 - - - +
424C SER* 2.9 46.4 + - - +
425C GLY 3.2 18.3 + - - +
427C VAL* 3.9 26.9 - - + +
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Residues in contact with HIS 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C ALA* 3.8 2.3 - - - -
216C SER 2.8 22.9 + - - -
217C ALA* 2.9 19.3 + - + +
219C TYR* 4.7 6.3 - + - -
231C ALA* 4.5 8.7 - - + -
232C GLU* 1.3 75.6 - - - +
234C SER* 1.3 59.5 + - - +
237C SER* 3.0 21.7 + - - +
238C LEU* 3.8 31.4 - - + +
266C ILE* 3.6 18.7 - - + +
364C THR* 2.7 30.4 + - + -
365C GLU 4.1 2.0 - - - -
366C THR 4.8 0.7 - - - -
367C GLY* 4.8 3.8 - - - -
421C GLY 3.7 19.1 - - - -
423C PHE* 3.5 22.8 - - + +
424C SER* 4.4 3.6 - - - +
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Residues in contact with SER 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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38C GLN* 5.5 1.7 + - - -
212C SER 3.2 10.9 + - - -
213C GLN* 3.8 15.2 - - - +
214C GLU 3.2 15.0 - - - -
215C ALA* 4.4 0.2 - - - +
216C SER* 3.7 6.9 - - - -
233C HIS* 1.3 75.8 - - - +
235C TYR* 1.3 64.3 + - - +
236C SER* 3.2 8.1 + - - -
237C SER* 2.7 40.4 + - - -
238C LEU* 3.4 12.8 + - - +
418C ARG* 5.9 0.5 + - - -
424C SER* 4.0 11.8 + - - -
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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