Contacts of the helix formed by residues 258 - 263 (chain C) in PDB entry 2UZ1
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 258 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C TYR* 3.8 22.4 + - - -
256C LEU* 3.8 32.9 - - + +
257C VAL* 1.3 82.0 - - - +
259C ASN* 1.3 72.7 + - - +
261C TYR* 3.1 17.2 + - - +
283C ASN 5.4 1.3 - - - +
291C LEU* 3.7 13.0 - - + +
356C ARG* 3.2 15.2 + - - +
401C SER* 3.1 27.0 + - - +
402C GLU* 3.9 16.6 - - - +
552C GLU* 3.6 31.9 + - - +
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Residues in contact with ASN 259 (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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236C PHE* 4.3 6.1 - - + -
254C GLY 3.7 17.7 + - - +
256C LEU 2.9 14.6 + - - +
258C GLN* 1.3 83.1 - - - +
260C LEU* 1.3 59.5 + - - +
261C TYR* 3.1 2.7 + - - -
262C SER* 3.7 10.2 + - - -
263C PHE* 3.3 19.2 - - + -
352C LEU* 5.6 1.0 - - - +
353C ALA* 4.1 25.1 - - + +
356C ARG* 3.5 31.1 + - - +
402C GLU* 4.9 0.5 - - - +
405C SER* 3.6 27.6 + - - -
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Residues in contact with LEU 260 (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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208C VAL* 4.5 17.0 - - + -
210C VAL* 4.6 3.1 - - + -
236C PHE* 3.6 35.0 - - + -
257C VAL* 3.0 34.4 + - + +
259C ASN* 1.3 76.2 - - - +
261C TYR* 1.3 63.5 + - - +
262C SER 3.3 0.9 - - - -
263C PHE* 3.1 35.3 + - + +
264C ALA 4.7 0.7 + - - -
270C PRO* 3.9 24.2 - - + -
273C VAL* 5.8 0.2 - - + -
290C GLN 3.8 6.2 - - - +
291C LEU* 3.5 32.7 - - - +
292C ILE* 4.5 6.3 - - + -
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Residues in contact with TYR 261 (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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258C GLN 3.1 15.4 + - - +
259C ASN 3.1 1.0 - - - -
260C LEU* 1.3 78.2 - - - +
262C SER* 1.3 68.3 + - - +
263C PHE 3.3 3.6 + - - -
264C ALA* 4.3 6.9 + - - +
265C LYS* 5.3 1.0 + - - +
290C GLN* 3.7 31.8 - - + +
291C LEU* 3.4 15.0 - - + +
356C ARG* 4.0 11.2 - - - +
552C GLU* 5.6 0.2 - - - +
555C ILE* 3.7 50.9 - - + +
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Residues in contact with SER 262 (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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259C ASN 3.7 11.2 + - - -
260C LEU 3.3 0.4 - - - -
261C TYR* 1.3 87.1 - - - +
263C PHE* 1.3 69.2 + - - +
264C ALA 3.5 0.7 - - - -
265C LYS* 3.7 10.6 + - - +
266C ALA* 3.4 19.8 + - - +
352C LEU* 4.3 21.9 + - - +
356C ARG* 5.4 8.6 + - - +
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Residues in contact with PHE 263 (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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236C PHE* 4.2 7.0 - + - -
259C ASN* 3.3 28.7 - - + -
260C LEU* 3.1 38.9 + - + +
261C TYR 3.2 0.2 - - - -
262C SER* 1.3 77.1 - - - +
264C ALA* 1.3 64.1 + - - +
266C ALA* 3.0 12.4 + - - +
268C ALA* 2.9 47.9 + - + +
269C ALA* 3.8 7.2 - - - -
270C PRO* 4.2 5.2 - - + -
345C TRP* 3.6 22.7 - + - -
349C VAL* 3.9 30.3 - - + -
352C LEU* 3.7 35.2 - - + -
353C ALA 5.6 0.4 - - - -
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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