Contacts of the helix formed by residues 267 - 271 (chain C) in PDB entry 4LXZ
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 GLY 267 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C ILE 3.7 0.3 - - - +
181C ASP* 3.4 31.7 - - - +
265C GLN* 2.9 13.8 + - - -
266C CYS* 1.3 70.2 - - - +
268C ALA* 1.3 52.4 + - - -
269C ASP* 3.4 8.5 - - - -
270C SER* 3.2 9.7 + - - -
286C HIS* 2.8 23.7 + - - -
304C GLY 3.7 0.8 + - - -
305C GLY* 4.0 4.7 - - - -
306C GLY 3.6 11.4 - - - -
317C TRP* 4.6 0.2 - - - -
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Residues in contact with ALA 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C CYS 3.1 0.8 + - - -
267C GLY* 1.3 68.2 - - - -
269C ASP* 1.3 55.7 + - - +
270C SER 3.1 5.4 - - - -
271C LEU* 3.3 40.0 + - + +
274C ASP* 4.1 3.8 - - - +
286C HIS* 3.9 8.5 - - - -
306C GLY 2.9 12.5 + - - +
307C GLY* 3.8 3.1 - - - -
313C VAL* 4.0 25.1 - - + +
316C CYS* 4.3 5.8 - - + -
317C TRP* 4.0 19.5 - - + +
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Residues in contact with ASP 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C ASP* 3.0 19.1 - - - +
182C ILE* 3.0 27.5 + - + +
183C HIS* 3.1 4.0 + - + -
267C GLY 3.9 0.2 - - - -
268C ALA* 1.3 70.1 - - - +
270C SER* 1.3 57.2 + - - +
271C LEU 3.2 6.1 + - - +
274C ASP* 3.4 37.6 - - - +
277C GLY* 3.6 14.4 - - - +
279C PHE* 5.0 0.2 - - - +
306C GLY* 3.4 4.9 - - - -
307C GLY* 3.5 16.8 - - - +
308C TYR* 3.4 4.2 - - + -
401C ZN 2.0 33.2 - - - -
406C SHH 2.9 8.5 - - - +
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Residues in contact with SER 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C ILE 2.9 27.9 + - - -
182C ILE* 3.9 11.4 - - - -
242C TYR* 5.6 0.4 - - - -
267C GLY 3.2 1.4 + - - -
269C ASP* 1.3 78.1 + - - +
271C LEU* 1.4 59.5 + - - +
279C PHE* 3.2 40.7 - - - +
281C LEU* 3.4 24.8 - - - +
286C HIS* 3.1 25.5 + - - -
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Residues in contact with LEU 271 (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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268C ALA* 3.3 20.6 - - + +
269C ASP 3.2 1.7 - - - +
270C SER* 1.4 81.2 - - - +
272C SER* 1.3 71.6 + - - +
273C GLY 3.5 0.2 + - - -
274C ASP* 3.2 20.2 + - + +
277C GLY 5.5 0.3 - - - -
279C PHE 3.9 6.6 + - - +
281C LEU* 3.6 4.5 - - + +
282C THR 3.4 35.0 - - - +
283C VAL* 3.8 10.3 - - + +
286C HIS* 3.7 20.6 - - + -
312C ASN* 3.6 39.7 - - + +
313C VAL* 5.9 0.2 - - + -
316C CYS* 3.7 17.0 - - + -
350C ILE* 4.4 2.7 - - + -
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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