Contacts of the helix formed by residues 307 - 320 (chain A) in PDB entry 5JLH
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 GLY 307 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A VAL* 4.2 14.3 - - - +
220A LEU* 4.6 8.9 - - - +
305A TYR 3.3 1.2 + - - -
306A PRO* 1.3 72.4 - - - +
308A ILE* 1.3 64.1 + - - +
309A ALA* 3.3 2.7 - - - +
310A ASP* 3.4 19.6 + - - +
311A ARG* 3.1 22.2 + - - +
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Residues in contact with ILE 308 (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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218A VAL* 3.6 22.9 - - + -
260A LEU* 5.0 5.4 - - + -
261A PHE* 4.4 10.3 - - + -
273A ILE* 5.1 5.8 - - + -
298A LEU* 4.1 15.9 - - + -
302A THR 3.8 3.1 - - - +
303A THR* 3.1 46.0 - - + +
305A TYR* 3.4 35.0 + - + +
306A PRO 3.4 0.6 - - - -
307A GLY* 1.3 77.5 - - - +
309A ALA* 1.3 64.1 + - - +
311A ARG* 3.2 4.5 + - - +
312A MET* 2.9 35.4 + - + +
334A ARG* 6.5 0.2 - - - -
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Residues in contact with ALA 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 4.3 8.5 - - + -
307A GLY* 4.4 0.8 - - - -
308A ILE* 1.3 81.1 - - - +
310A ASP* 1.3 68.0 + - - +
312A MET* 3.3 5.9 + - - +
313A GLN* 2.9 26.0 + - - +
328A ILE* 3.9 13.8 - - + +
330A ALA* 4.3 24.0 - - + -
334A ARG* 5.2 5.2 - - - +
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Residues in contact with ASP 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A LEU* 4.3 28.1 - - + +
307A GLY* 3.4 17.6 + - - +
308A ILE 3.2 0.4 - - - -
309A ALA* 1.3 80.4 - - - +
311A ARG* 1.3 64.3 + - - +
313A GLN* 3.1 12.3 + - - +
314A LYS* 2.9 23.8 + - - +
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Residues in contact with ARG 311 (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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218A VAL* 3.4 19.7 - - + -
219A ALA 3.3 26.3 + - - +
220A LEU* 5.0 3.1 - - - +
221A ASP* 4.2 1.8 + - - +
222A PHE* 3.9 17.2 - - - +
258A GLU* 3.1 26.8 + - - -
261A PHE* 3.4 25.3 - - + +
262A GLN* 4.5 8.5 - - - +
307A GLY 3.1 14.8 + - - +
308A ILE 3.2 3.3 + - - +
310A ASP* 1.3 80.7 - - - +
312A MET* 1.3 61.8 + - - +
314A LYS* 3.2 40.0 + - - +
315A GLU* 2.8 54.6 + - - +
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Residues in contact with MET 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A MET* 5.1 4.7 - - + -
261A PHE* 3.6 13.5 - - + -
273A ILE* 3.5 31.2 - - + -
274A HIS* 3.8 14.1 - - - +
277A THR* 3.9 21.5 - - + +
296A THR* 5.3 6.1 - - + -
298A LEU* 4.9 18.2 - - + -
308A ILE* 2.9 31.5 + - + +
309A ALA* 3.6 5.8 - - - +
311A ARG* 1.3 76.1 - - - +
313A GLN* 1.3 56.3 + - - +
315A GLU* 4.1 3.4 - - - -
316A ILE* 2.9 53.4 + - + +
328A ILE* 3.7 13.5 - - + -
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Residues in contact with GLN 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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309A ALA* 2.9 14.6 + - - +
310A ASP* 3.1 15.5 + - - +
312A MET* 1.3 77.9 - - - +
314A LYS* 1.3 59.4 + - - +
316A ILE* 4.4 1.4 - - - +
317A THR* 2.6 39.7 + - - +
326A ILE* 3.5 26.4 + - + +
327A LYS* 4.8 3.6 - - - +
328A ILE* 3.3 24.0 + - + +
385F ASN* 5.1 10.3 + - - +
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Residues in contact with LYS 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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220A LEU* 3.0 31.2 - - + +
221A ASP* 4.4 8.8 + - - +
310A ASP 2.9 12.1 + - - +
311A ARG* 3.2 49.2 - - - +
313A GLN* 1.3 77.0 - - - +
315A GLU* 1.3 72.7 + - - +
317A THR* 3.8 4.3 - - - -
318A ALA* 2.9 30.0 + - - +
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Residues in contact with GLU 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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261A PHE* 3.0 25.2 - - - -
274A HIS* 2.9 46.6 - - + +
311A ARG* 2.8 55.5 + - - +
312A MET* 3.9 2.4 - - - +
314A LYS* 1.3 91.6 - - - +
316A ILE* 1.3 67.0 + - - +
318A ALA* 3.1 7.3 + - - +
319A LEU* 2.9 27.9 + - + +
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Residues in contact with ILE 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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274A HIS* 4.1 18.6 - - + +
277A THR* 3.9 26.0 - - + -
278A PHE* 3.9 15.4 - - + -
281A ILE* 5.9 1.8 - - + -
293A TYR* 4.3 18.8 - - + -
296A THR* 5.1 8.1 - - + +
312A MET* 2.9 43.5 + - + +
313A GLN* 4.4 1.3 - - - +
315A GLU* 1.3 72.9 - - - +
317A THR* 1.3 61.4 + - - +
319A LEU* 3.1 2.7 + - + +
320A ALA* 2.8 29.5 + - - +
326A ILE* 3.6 26.0 - - + -
328A ILE* 5.0 6.3 - - + -
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Residues in contact with THR 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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313A GLN* 2.6 31.2 + - - +
314A LYS* 3.8 5.2 - - - -
316A ILE* 1.3 77.6 - - - +
318A ALA* 1.3 63.7 + - - +
320A ALA* 3.4 15.7 - - - +
321A PRO 5.1 0.6 - - - -
322A SER* 4.9 16.8 + - - -
324A MET 6.0 0.4 - - - +
326A ILE* 3.9 28.3 + - + +
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Residues in contact with ALA 318 (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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314A LYS 2.9 20.3 + - - +
315A GLU* 3.4 8.5 - - - +
316A ILE 3.1 0.2 - - - -
317A THR* 1.3 78.2 - - - +
319A LEU* 1.3 66.7 + - + +
320A ALA 4.0 2.9 - - - +
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Residues in contact with LEU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A HIS* 4.0 26.2 - - + -
275A GLU* 4.3 16.4 - - + +
278A PHE* 3.3 39.9 - - + -
315A GLU 2.9 18.1 + - - +
316A ILE* 5.2 0.4 - - - -
318A ALA* 1.3 82.9 - - + +
320A ALA* 1.3 59.7 + - - +
321A PRO* 4.7 0.5 - - - +
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Residues in contact with ALA 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A PHE* 3.4 15.5 - - + -
293A TYR* 3.7 21.5 - - + -
316A ILE 2.8 21.8 + - - +
317A THR* 3.4 11.6 + - - +
318A ALA 3.5 2.8 - - - +
319A LEU* 1.3 76.2 - - - +
321A PRO* 1.3 84.6 - - + +
322A SER* 3.2 3.6 + - - -
324A MET* 6.0 0.2 - - + -
326A ILE* 4.5 6.3 - - + -
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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