Contacts of the helix formed by residues 312 - 317 (chain A) in PDB entry 5IXM
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 TYR 312 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286A ARG* 5.2 7.4 - - - +
311A ASP* 1.3 79.0 + - - +
313A SER* 1.3 69.9 + - - +
315A LEU* 3.2 31.9 - - + +
316A PHE* 4.0 18.6 - + - -
336A GLY* 3.8 17.2 - - - -
337A LEU 3.9 2.4 + - - -
338A THR* 3.4 17.1 + - - -
353A SER* 3.7 19.7 - - - -
354A VAL 3.6 5.4 - - - -
355A GLY* 3.5 25.4 - - - -
383A ALA* 3.7 21.9 - - - +
384A GLY* 4.5 11.1 + - - +
385A ASP* 3.2 31.2 - - + +
401A GLN* 5.5 0.4 - - - +
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Residues in contact with SER 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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286A ARG* 5.5 2.1 + - - +
311A ASP* 3.3 14.7 + - - -
312A TYR* 1.3 82.7 - - - +
314A GLY* 1.3 57.6 - - - +
315A LEU 2.8 11.7 + - - -
316A PHE* 2.9 23.4 + - - +
317A ARG* 3.9 2.0 + - - +
104B ARG* 3.6 25.0 + - - -
126B GLU* 4.8 4.7 - - - -
130B GLN* 4.4 5.2 + - - -
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Residues in contact with GLY 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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310A SER* 4.2 10.8 - - - -
311A ASP* 3.2 20.0 + - - -
313A SER* 1.3 76.3 - - - +
315A LEU* 1.3 61.5 + - - +
316A PHE 3.1 0.4 - - - -
317A ARG* 3.2 51.7 + - - +
357A ILE* 5.3 1.2 - - - +
126B GLU* 5.0 1.1 + - - -
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Residues in contact with LEU 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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288A GLN* 4.2 0.7 + - - -
310A SER* 4.7 3.8 - - - -
311A ASP 3.5 9.0 + - - +
312A TYR* 3.2 31.2 - - + +
313A SER 2.8 0.6 + - - -
314A GLY* 1.3 77.8 - - - +
316A PHE* 1.3 70.2 + - + +
317A ARG 3.3 4.0 + - - +
332A GLN* 5.5 1.2 + - - -
334A SER* 3.0 23.7 + - - -
335A THR 4.9 0.4 - - - +
355A GLY* 3.5 35.9 - - - +
356A GLN 3.8 5.4 - - - +
357A ILE* 3.7 35.1 - - + +
381A VAL* 3.7 21.3 - - + -
383A ALA* 3.9 15.0 - - + +
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Residues in contact with PHE 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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262A LYS* 5.1 2.9 + - - -
264A ASP* 5.1 0.2 - - - +
286A ARG* 3.3 70.3 + - + +
288A GLN* 3.2 42.8 - - + +
312A TYR* 4.0 24.7 - + - -
313A SER* 2.9 16.7 + - - +
315A LEU* 1.3 88.6 - - + +
317A ARG* 1.3 62.5 + - - +
318A ASP* 3.6 1.6 + - - +
334A SER* 3.4 26.7 - - - -
335A THR 4.0 4.3 - - - -
336A GLY* 3.9 23.6 - - - -
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Residues in contact with ARG 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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288A GLN* 5.2 0.9 + - - -
290A LEU* 4.7 4.2 - - - +
308A MET* 3.8 28.8 - - - +
309A GLN 2.9 35.2 + - - -
310A SER* 3.5 14.5 - - - +
311A ASP* 5.1 1.8 + - - -
313A SER 3.9 1.2 + - - -
314A GLY* 3.2 30.0 + - - +
315A LEU 4.3 3.5 - - - +
316A PHE* 1.3 79.0 - - - +
318A ASP* 1.3 67.8 + - - +
319A ARG* 3.2 34.2 + - + +
332A GLN* 5.3 4.7 + - - -
122B VAL* 4.4 12.3 - - - -
123B LEU* 4.6 3.2 - - - +
126B GLU* 2.4 51.3 + - - +
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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