Contacts of the helix formed by residues 311 - 320 (chain A) in PDB entry 2Q41
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 ASN 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296A ILE 4.5 6.7 - - - -
297A ASP 5.0 8.5 - - - +
310A TYR* 1.3 95.9 - - - +
312A ALA* 1.3 63.3 + - - +
313A GLU* 2.8 31.2 + - - +
314A ILE* 2.8 36.7 + - - +
315A HIS 3.2 17.3 + - - -
321D LEU 3.6 4.8 + - - -
323D SER* 3.5 24.0 + - - +
326D LYS* 4.0 21.1 - - + +
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Residues in contact with ALA 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A PRO* 4.9 5.3 - - + +
295A PRO* 4.1 27.5 - - + +
296A ILE 5.2 1.6 + - - -
297A ASP* 6.0 3.2 - - - +
310A TYR* 4.5 0.4 - - - -
311A ASN* 1.3 73.7 - - - +
313A GLU* 1.3 65.5 + - + +
315A HIS* 3.7 7.6 + - - +
316A SER* 3.5 22.3 + - - -
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Residues in contact with GLU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A ASN* 2.8 12.9 + - - +
312A ALA* 1.3 72.3 - - + +
314A ILE* 1.3 55.9 + - + +
316A SER* 3.3 4.1 + - - -
317A ALA* 2.8 38.5 + - - +
290D LYS* 4.5 10.2 + - - +
319D PHE 4.2 15.0 - - - +
320D CYS* 3.9 25.9 - - + -
321D LEU 4.7 1.0 + - - +
326D LYS* 2.9 38.4 + - - +
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Residues in contact with ILE 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A MSE 3.9 33.9 - - + -
265A THR* 5.2 1.8 - - - +
309A PHE* 4.1 12.8 - - + +
310A TYR* 4.5 4.9 - - + -
311A ASN* 2.8 42.6 + - - +
313A GLU* 1.3 75.9 - - + +
315A HIS* 1.3 58.8 + - - +
317A ALA* 4.2 5.4 - - - -
318A ALA* 2.6 39.3 + - + +
264D TRP* 5.9 2.5 - - + -
320D CYS 3.1 14.8 - - - +
321D LEU 2.8 31.0 - - - +
322D PRO* 3.6 15.0 - - + -
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Residues in contact with HIS 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A HIS 4.3 1.6 - - - -
113A LEU* 3.2 48.5 + - + +
116A CYS* 4.4 0.7 - - + -
117A SER* 3.3 9.1 + - - -
289A PHE* 2.7 28.7 + - - +
292A PRO* 3.1 37.3 - - + +
310A TYR* 2.8 31.2 + - + +
311A ASN 3.2 12.9 + - - +
312A ALA 3.9 6.1 - - - +
313A GLU 3.3 0.2 - - - -
314A ILE* 1.3 79.8 - - - +
316A SER* 1.3 58.8 + - - +
318A ALA* 3.5 4.2 - - - +
319A PHE* 3.1 20.5 - + - -
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Residues in contact with SER 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A LYS* 2.7 26.8 + - - +
291A HIS* 4.5 8.0 - - - -
292A PRO* 4.4 4.5 - - - +
312A ALA 3.5 11.0 + - - -
313A GLU* 3.3 6.6 + - - -
314A ILE 3.2 0.2 - - - -
315A HIS* 1.3 74.4 - - - +
317A ALA* 1.3 68.0 + - - +
318A ALA 3.1 1.1 - - - -
319A PHE* 3.2 20.4 + - - +
320A CYS* 3.9 7.1 + - - -
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Residues in contact with ALA 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A TRP* 5.0 0.9 + - - -
313A GLU 2.8 23.3 + - - +
314A ILE* 3.9 4.5 - - - +
316A SER* 1.3 73.0 - - - +
318A ALA* 1.3 65.2 + - - +
319A PHE 2.8 2.1 + - - -
320A CYS* 2.8 30.8 + - - +
317D ALA* 4.1 16.4 - - + +
320D CYS* 3.6 29.8 - - + +
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Residues in contact with ALA 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A MSE 5.0 3.8 - - - -
113A LEU* 4.5 11.4 - - + -
263A ALA* 4.2 11.4 - - + -
264A TRP* 2.8 56.4 + - - +
265A THR* 5.6 0.9 - - - +
314A ILE* 2.6 29.5 + - + +
315A HIS* 3.5 11.4 - - - +
317A ALA* 1.3 72.4 - - - +
319A PHE* 1.3 55.5 + - - +
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Residues in contact with PHE 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LEU* 4.7 2.5 - - + -
261A ASN* 3.5 30.3 - - + -
262A TYR 3.7 11.4 - - - +
263A ALA* 3.5 30.5 - - + +
279A LEU* 4.3 11.0 - - + -
289A PHE* 3.1 41.3 - - + -
290A LYS* 4.1 36.4 + - + +
315A HIS* 3.1 33.7 - + - -
316A SER 3.2 9.3 + - - +
317A ALA 2.8 4.4 + - - -
318A ALA* 1.3 74.8 - - - +
320A CYS* 1.3 52.5 + - - +
321A LEU* 2.8 34.7 + - - +
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Residues in contact with CYS 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A TRP* 2.9 18.1 + - - -
316A SER 4.1 9.0 - - - -
317A ALA* 2.8 26.2 + - - +
319A PHE* 1.3 68.3 - - - +
321A LEU* 1.3 60.5 + - - +
313D GLU* 3.4 51.6 - - + +
314D ILE* 3.3 13.0 - - - +
316D SER* 5.8 1.1 - - - -
317D ALA* 4.0 11.4 - - + +
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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