Contacts of the helix formed by residues 310 - 318 (chain K) in PDB entry 3IXS
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 310 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252K GLY 3.5 12.1 - - - -
253K ASN* 4.5 8.7 - - - -
254K ALA 3.3 7.9 - - - -
255K THR* 4.1 5.2 - - - +
308K SER 3.4 4.6 + - - -
309K PHE* 1.3 76.4 - - - +
311K LEU* 1.3 63.8 + - - +
312K GLU* 3.5 10.3 + - - +
313K LEU* 2.9 29.4 + - - +
314K VAL* 3.0 19.9 + - - +
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Residues in contact with LEU 311 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226K ILE* 4.0 23.7 - - + +
228K LEU* 3.9 24.9 - - + -
250K THR* 3.5 29.2 - - + -
251K SER 4.1 3.4 - - - +
252K GLY* 3.3 6.0 + - - +
254K ALA* 2.8 44.6 + - + +
255K THR 3.8 9.0 - - - +
256K VAL* 4.3 2.9 - - + +
259K LEU* 3.8 26.2 - - + -
310K SER* 1.3 73.2 - - - +
312K GLU* 1.3 56.9 - - - +
314K VAL* 3.7 9.3 - - + +
315K SER* 2.8 31.5 + - - -
325K MET* 4.5 6.5 - - - +
327K LEU* 5.6 0.9 - - + -
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Residues in contact with GLU 312 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226K ILE* 4.0 10.1 - - + +
252K GLY* 3.0 23.3 + - - +
253K ASN* 6.0 0.5 - - - -
310K SER* 3.6 7.1 + - - +
311K LEU* 1.3 77.7 - - - +
313K LEU* 1.3 58.0 + - - +
315K SER* 3.3 3.5 + - - -
316K GLU* 3.0 56.1 + - + +
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Residues in contact with LEU 313 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309K PHE* 4.0 35.9 - - + -
310K SER* 2.9 23.7 + - - +
312K GLU* 1.3 73.7 - - - +
314K VAL* 1.3 62.8 + - - +
316K GLU* 3.2 11.3 + - - +
317K LYS* 2.8 49.7 + - + +
318K TYR* 4.1 18.6 - - + -
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Residues in contact with VAL 314 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256K VAL* 4.2 15.3 - - + -
295K ILE* 3.6 27.1 - - + -
305K LEU* 4.1 15.3 - - + -
309K PHE* 3.8 26.7 - - + -
310K SER 3.0 16.8 + - - +
311K LEU* 3.7 10.5 - - + +
313K LEU* 1.3 74.8 - - - +
315K SER* 1.3 59.1 + - - +
318K TYR* 2.8 37.4 + - + -
319K TRP 3.2 6.6 + - - -
325K MET* 3.6 15.7 - - + -
327K LEU* 4.4 2.5 - - + -
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Residues in contact with SER 315 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226K ILE* 4.6 15.2 - - - +
311K LEU 2.8 17.3 + - - -
312K GLU* 3.5 7.0 - - - -
314K VAL* 1.3 77.3 - - - +
316K GLU* 1.3 60.7 + - - +
319K TRP* 2.7 32.7 - - - +
325K MET* 3.4 20.3 - - - +
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Residues in contact with GLU 316 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312K GLU* 3.0 43.5 + - + +
313K LEU* 3.8 11.9 - - - +
315K SER* 1.3 77.5 - - - +
317K LYS* 1.3 62.2 + - + +
319K TRP 4.6 2.9 - - - +
320K LYS* 5.6 2.9 - - - +
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Residues in contact with LYS 317 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309K PHE* 4.5 9.5 - - - -
313K LEU* 2.8 33.8 + - + +
316K GLU* 1.3 75.6 - - + +
318K TYR* 1.3 105.6 + - + +
319K TRP 3.7 0.4 - - - -
320K LYS* 3.8 17.7 + - - -
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Residues in contact with TYR 318 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295K ILE* 3.5 35.8 - - + +
297K THR* 6.1 1.6 - - + -
303K THR* 4.3 26.8 - - + +
304K VAL 5.3 1.4 + - - -
305K LEU* 4.0 19.1 - - + -
309K PHE* 3.4 31.8 - + - -
313K LEU* 4.1 3.6 - - + -
314K VAL* 2.8 23.9 + - + +
317K LYS* 1.3 125.3 + - + +
319K TRP* 1.3 61.8 + - - +
320K LYS* 4.0 15.4 + - - +
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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