Contacts of the helix formed by residues 311 - 318 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321B LEU 3.1 24.7 + - - +
322B PRO* 3.9 0.4 - - - +
323B SER* 3.1 28.9 + - - +
326B LYS* 4.4 22.2 - - - +
296C ILE 4.4 6.1 - - - +
297C ASP* 6.5 0.2 - - - -
307C LEU* 5.1 0.7 - - + -
309C PHE 3.7 3.8 + - - -
310C TYR* 1.3 88.4 - - - +
312C ALA* 1.3 65.0 + - - +
313C GLU* 3.1 12.4 + - - +
314C ILE* 2.8 35.3 + - - +
315C HIS* 3.1 5.9 + - - +
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Residues in contact with ALA 312 (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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292C PRO* 4.6 6.2 - - + +
295C PRO* 3.5 33.7 - - + +
296C ILE 4.7 2.0 + - - -
310C TYR* 4.2 3.0 - - - -
311C ASN* 1.3 72.8 - - - +
313C GLU* 1.3 63.1 + - + +
315C HIS* 3.1 18.7 - - - +
316C SER* 3.3 11.6 + - - -
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Residues in contact with GLU 313 (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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290B LYS* 5.9 0.5 + - - -
319B PHE 4.7 3.3 - - - +
320B CYS* 3.9 34.7 - - + -
321B LEU 5.2 1.9 + - - +
326B LYS* 4.3 24.5 + - - +
311C ASN* 3.1 9.6 + - - +
312C ALA* 1.3 73.3 - - + +
314C ILE* 1.3 58.4 + - - +
315C HIS 3.0 5.0 + - - -
316C SER* 3.3 6.8 + - - -
317C ALA* 3.0 27.0 + - - +
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Residues in contact with ILE 314 (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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264B TRP* 4.3 17.7 - - + +
320B CYS* 3.1 31.3 - - + +
321B LEU 4.3 8.3 - - - +
322B PRO* 4.3 1.6 - - + -
109C MSE 3.4 31.0 - - + +
265C THR* 5.4 0.2 - - - +
309C PHE* 3.8 16.4 - - + +
310C TYR* 3.8 8.1 - - + -
311C ASN* 2.8 50.4 + - - +
313C GLU* 1.3 76.2 - - - +
315C HIS* 1.3 62.5 + - - +
317C ALA* 3.8 8.3 - - + -
318C ALA* 3.2 15.8 + - - +
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Residues in contact with HIS 315 (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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109C MSE 4.7 1.3 - - - -
112C HIS 3.9 2.9 - - - -
113C LEU* 3.5 46.2 + - + +
116C CYS* 4.6 1.1 - - + -
117C SER* 3.7 6.2 + - - -
289C PHE 2.7 28.3 + - - -
290C LYS 3.8 1.8 - - - -
292C PRO* 3.6 28.7 - - + +
310C TYR* 2.5 35.5 + - + +
311C ASN 3.1 10.7 + - - +
312C ALA* 3.1 14.8 - - - +
313C GLU 3.0 0.4 - - - -
314C ILE* 1.3 78.9 - - - +
316C SER* 1.3 64.8 + - - +
318C ALA* 3.2 18.7 + - - +
319C PHE* 3.5 6.0 - + - -
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Residues in contact with SER 316 (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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290C LYS* 2.8 28.1 + - - +
291C HIS* 4.5 10.1 - - - -
292C PRO* 4.1 5.0 - - - +
312C ALA 3.3 8.0 + - - -
313C GLU* 3.3 8.5 + - - -
315C HIS* 1.3 77.2 - - - +
317C ALA* 1.3 63.3 + - - +
318C ALA 3.1 0.9 + - - -
319C PHE* 3.2 17.2 + - - +
320C CYS* 3.6 12.3 - - - -
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Residues in contact with ALA 317 (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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317B ALA* 3.9 19.4 - - + +
320B CYS* 3.7 24.6 - - + -
264C TRP* 4.6 2.9 + - - -
313C GLU 3.0 17.4 + - - +
314C ILE* 3.9 12.1 - - + +
316C SER* 1.3 77.3 - - - +
318C ALA* 1.3 62.2 + - - +
320C CYS* 3.1 30.2 + - - +
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Residues in contact with ALA 318 (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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109C MSE 4.1 13.2 - - + -
113C LEU* 4.4 6.3 - - + -
263C ALA* 3.3 13.7 - - + -
264C TRP* 2.8 56.3 + - - +
314C ILE 3.2 12.5 + - - +
315C HIS 3.2 15.4 + - - +
316C SER 3.1 0.4 - - - -
317C ALA* 1.3 78.8 - - - +
319C PHE* 1.3 57.3 + - + +
320C CYS 3.3 1.1 - - - -
321C LEU* 4.2 0.3 - - - +
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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