Contacts of the helix formed by residues 262 - 266 (chain C) in PDB entry 3DLX
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 PRO 262 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C ASN* 3.5 7.9 - - - +
236C LYS* 5.8 0.2 - - - -
259C ILE* 3.7 7.8 - - + +
260C HIS 3.9 7.2 - - - +
261C ILE* 1.3 98.5 - - + +
263C GLN* 1.3 65.4 + - - +
264C ILE* 3.0 7.2 + - + -
265C TYR* 3.2 25.2 + - + +
266C VAL* 3.9 0.5 - - - +
348D LEU* 4.2 14.8 - - + -
378D SER* 3.6 25.8 - - - +
380D PHE* 4.4 8.7 - - + -
384D GLU* 5.6 2.7 - - + +
388D MET* 4.0 20.4 - - + -
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Residues in contact with GLN 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C THR* 3.8 2.2 + - - +
218C ALA* 3.3 45.1 + - - +
219C GLY 3.5 15.7 - - - -
220C ASN* 2.9 18.2 + - - +
261C ILE 3.8 0.4 + - - -
262C PRO* 1.3 70.7 - - - +
264C ILE* 1.3 63.8 + - - +
266C VAL 3.0 21.9 + - - +
318D TYR* 3.1 24.0 + - + +
340D HIS* 3.7 31.0 + - - -
348D LEU* 4.0 18.7 - - + +
349D GLY* 5.5 1.6 - - - -
376D GLY 3.5 17.7 + - - +
378D SER* 5.5 0.7 + - - -
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Residues in contact with ILE 264 (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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262C PRO* 3.0 3.0 + - + +
263C GLN* 1.3 81.6 - - - +
265C TYR* 1.3 82.2 + - + +
266C VAL 3.5 0.4 + - - -
267C HIS* 4.0 14.0 + - - -
318D TYR* 3.6 47.5 - - + -
342D GLN* 5.6 0.2 - - + -
348D LEU* 3.8 17.0 - - + +
388D MET* 4.0 29.4 - - + -
393D HIS* 3.3 46.7 + - + +
394D VAL* 4.3 7.2 - - + +
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Residues in contact with TYR 265 (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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149C GLY 5.1 0.7 + - - -
235C CYS* 3.2 18.0 - - - +
236C LYS* 3.7 34.0 - - + +
241C THR* 2.7 28.2 + - - +
261C ILE* 3.9 24.7 - - + -
262C PRO* 3.2 18.6 + - + +
263C GLN 3.1 0.4 - - - -
264C ILE* 1.3 87.1 - - + +
266C VAL* 1.3 52.6 + - - +
267C HIS* 3.9 7.0 + - - -
384D GLU* 2.5 31.0 + - - -
387D ALA* 4.4 2.9 - - - +
388D MET* 3.7 35.5 + - + +
393D HIS* 3.4 46.2 + + + -
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Residues in contact with VAL 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C THR* 3.0 36.4 + - + +
219C GLY 3.4 27.4 - - - +
221C VAL* 4.0 9.9 - - + -
235C CYS* 5.1 0.9 - - - -
241C THR* 3.6 3.6 - - - -
243C VAL* 4.1 20.4 - - + -
261C ILE* 3.4 29.8 - - + -
262C PRO 3.9 2.7 - - - +
263C GLN 3.0 9.0 + - - +
264C ILE 3.5 0.4 - - - -
265C TYR* 1.3 78.8 - - - +
267C HIS* 1.3 62.7 + - - +
268C ARG 4.0 13.2 - - - +
269C LEU* 4.2 9.6 - - + -
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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
------------------------------------------------------------
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