Contacts of the helix formed by residues 311 - 316 (chain D) in PDB entry 2OYQ
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 LYS 311 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310D SER* 1.3 79.6 - - - +
312D LEU* 1.3 58.1 + - - +
313D ARG 3.3 2.5 - - - -
314D GLU* 3.3 32.6 + - + +
315D SER* 2.8 34.6 + - - +
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Residues in contact with LEU 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305D TYR* 4.6 15.0 - - + -
306D ASP* 6.1 2.9 - - - -
308D PRO 4.5 5.6 - - - +
309D ILE* 4.2 24.5 - - + +
310D SER 3.3 4.2 + - - +
311D LYS* 1.3 77.6 - - - +
313D ARG* 1.3 61.3 + - - +
315D SER* 4.0 4.5 - - - -
316D ASN* 3.2 31.9 + - - +
320D TYR* 3.3 10.5 - - + +
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Residues in contact with ARG 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D THR* 3.8 31.4 - - + +
134D ASP* 4.0 25.2 + - + +
150D ASP* 4.3 3.8 + - - -
151D LEU 2.7 30.4 + - - -
152D LEU* 4.6 3.0 + - - +
154D SER* 5.9 2.7 - - - -
157D GLY 4.8 10.8 + - - -
159D VAL* 3.4 39.3 - - - +
160D GLU 4.7 4.8 + - - -
311D LYS 3.3 0.4 - - - -
312D LEU* 1.3 79.0 - - - +
314D GLU* 1.3 64.4 + - + +
317D HIS* 3.4 22.7 - - - +
320D TYR* 3.5 17.2 - - + +
321D ILE* 3.4 34.8 - - + +
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Residues in contact with GLU 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D THR* 6.1 1.2 - - - -
156D TYR* 4.8 5.5 - - - +
157D GLY* 4.2 27.3 - - - -
159D VAL* 5.1 7.3 - - - +
310D SER 5.3 1.0 - - - +
311D LYS* 3.3 29.5 + - + +
312D LEU 3.2 0.4 - - - -
313D ARG* 1.3 83.3 - - + +
315D SER* 1.3 65.5 + - - +
317D HIS* 4.2 6.4 + - - +
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Residues in contact with SER 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306D ASP* 4.4 17.7 - - - +
311D LYS* 2.8 25.9 + - - -
312D LEU* 4.0 3.8 + - - -
314D GLU* 1.3 79.2 - - - +
316D ASN* 1.3 63.5 + - - +
317D HIS 3.9 1.0 + - - -
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Residues in contact with ASN 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305D TYR* 6.1 3.4 - - + -
306D ASP* 5.6 9.6 - - + +
312D LEU* 3.2 13.9 + - - +
315D SER* 1.3 81.9 + - - +
317D HIS* 1.3 58.3 + - - +
318D GLN 3.4 2.7 - - - -
319D ARG* 3.1 19.0 + - + -
320D TYR* 2.9 23.7 + - - +
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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