Contacts of the helix formed by residues 307 - 315 (chain B) in PDB entry 2W9C
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 SER 307 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273B TYR* 3.5 2.3 + - - -
305B GLY 4.0 2.6 + - - -
306B ILE* 1.3 74.7 - - - +
308B LYS* 1.3 53.9 + - - +
309B GLU* 2.8 22.6 + - - +
310B THR* 2.6 37.3 + - - -
311B ALA 2.7 32.2 + - - -
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Residues in contact with LYS 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B ILE* 5.3 0.2 - - + -
270B GLU* 3.1 26.8 + - - +
273B TYR* 3.7 53.0 + - + +
274B TYR* 5.8 0.4 - - - +
307B SER* 1.3 71.2 - - - +
309B GLU* 1.3 75.5 + - + +
311B ALA* 3.1 1.6 + - - +
312B TYR* 2.9 47.7 + - + +
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Residues in contact with GLU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B SER* 2.8 27.2 - - - +
308B LYS* 1.3 89.3 + - - +
310B THR* 1.3 62.8 + - - +
311B ALA 3.0 0.2 + - - -
312B TYR* 3.1 15.2 + - - +
313B SER* 3.3 11.5 + - - -
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Residues in contact with THR 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B PHE* 4.5 26.0 - - + -
304B HIS* 5.2 10.2 - - + -
306B ILE* 4.0 13.5 - - + -
307B SER* 2.6 40.6 + - - -
309B GLU* 1.3 72.5 - - - +
311B ALA* 1.3 54.2 + - - -
313B SER* 3.4 6.1 - - - -
314B GLU* 2.8 35.1 + - + +
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Residues in contact with ALA 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B ILE* 3.7 10.8 - - + -
273B TYR* 3.4 34.3 - - + +
284B ILE* 4.6 5.6 - - - -
306B ILE* 4.0 6.5 - - + +
307B SER 2.7 12.2 + - - +
308B LYS 3.5 5.4 - - - +
310B THR* 1.3 68.7 - - - +
312B TYR* 1.3 53.7 + - - +
313B SER 2.7 15.5 + - - -
315B SER* 2.7 32.7 + - - -
337B PHE* 3.8 13.2 - - + -
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Residues in contact with TYR 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B PHE* 3.1 84.4 + + + +
269B ILE* 4.2 15.9 - - + +
270B GLU* 2.7 31.7 + - - +
308B LYS* 2.9 42.4 + - + +
309B GLU* 3.5 11.0 - - - +
311B ALA* 1.3 70.7 - - - +
313B SER* 1.3 56.0 + - - +
315B SER* 4.6 1.3 - - - -
316B VAL* 3.8 8.5 - - - +
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Residues in contact with SER 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B GLU 3.3 9.7 + - - -
310B THR* 3.4 12.1 - - - -
311B ALA 2.7 2.0 + - - -
312B TYR* 1.3 77.9 - - - +
314B GLU* 1.3 58.6 + - - -
315B SER 2.8 10.8 + - - -
316B VAL* 3.3 13.5 + - - +
317B LYS* 3.3 26.0 + - - -
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Residues in contact with GLU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B ILE* 5.1 11.0 - - + -
300B ARG* 2.7 41.7 + - + +
302B PHE* 3.7 29.8 - - + -
306B ILE* 6.4 0.2 - - + -
310B THR* 2.8 23.8 + - + +
311B ALA* 4.7 0.9 - - - +
313B SER* 1.3 73.2 + - - +
315B SER* 1.3 56.9 + - - +
317B LYS* 3.0 38.6 + - - +
318B LEU* 3.2 35.0 + - + +
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Residues in contact with SER 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B LEU* 4.0 13.9 - - - +
269B ILE* 3.0 27.0 - - - +
284B ILE* 3.6 18.7 - - - +
286B VAL* 4.3 11.5 - - - +
311B ALA 2.7 21.6 + - - -
312B TYR 4.6 2.5 - - - -
313B SER 2.8 1.6 + - - -
314B GLU* 1.3 76.2 - - - +
316B VAL* 1.3 57.0 + - - -
317B LYS 3.0 0.7 - - - -
318B LEU* 2.5 29.2 + - - +
319B LEU* 2.7 12.6 + - - +
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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
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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