Contacts of the helix formed by residues 309 - 323 (chain A) in PDB entry 5HJC
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 309 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307A LYS 3.4 3.6 + - - -
308A LEU* 1.3 76.6 - - - +
310A GLU* 1.3 60.4 + - - +
311A HIS 4.3 1.8 - - - -
312A LEU* 3.2 31.8 + - - +
313A ARG* 2.9 27.8 + - - +
501A EDO 3.8 16.9 + - - -
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Residues in contact with GLU 310 (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 SER* 1.3 73.8 - - - +
311A HIS* 1.3 68.8 + - + +
313A ARG* 3.3 33.0 + - - +
314A TYR* 3.2 19.8 + - - +
416A PRO* 4.5 19.2 - - - +
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Residues in contact with HIS 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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309A SER* 3.2 1.2 + - - -
310A GLU* 1.3 89.8 + - + +
312A LEU* 1.3 57.5 + - - +
314A TYR* 3.2 7.7 + - + +
315A CYS* 3.1 30.7 + - - -
373A ALA* 4.4 1.8 - - + -
415A MET* 3.8 30.3 - - + +
416A PRO* 2.8 34.6 + - - -
501A EDO 3.3 44.3 + - - +
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Residues in contact with LEU 312 (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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308A LEU* 3.9 26.4 - - + +
309A SER* 3.2 25.7 + - - +
311A HIS* 1.3 76.4 - - - +
313A ARG* 1.3 62.7 + - - +
315A CYS* 3.8 11.0 - - - +
316A ASP* 3.3 20.4 + - - +
365A MET* 3.8 17.4 - - + +
370A TYR* 3.3 35.2 - - + +
371A PRO 4.2 11.0 - - - +
372A ASP* 3.3 31.2 - - - +
373A ALA* 3.8 8.1 - - - +
376A PHE* 4.5 2.0 - - + -
501A EDO 5.0 0.7 - - - -
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Residues in contact with ARG 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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308A LEU* 3.9 30.8 + - + -
309A SER 2.9 9.5 + - - +
310A GLU* 3.4 40.0 + - - +
311A HIS 3.2 0.2 - - - -
312A LEU* 1.3 76.9 - - - +
314A TYR* 1.3 63.7 + - - +
316A ASP* 3.3 8.3 + - + +
317A SER* 3.1 20.6 + - - -
320A ARG* 5.5 0.7 + - - -
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Residues in contact with TYR 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 GLU 3.2 9.3 + - - +
311A HIS* 3.2 9.6 + - + +
313A ARG* 1.3 79.2 - - - +
315A CYS* 1.3 58.4 + - - +
317A SER* 3.2 14.0 + - - -
318A ILE* 3.1 51.5 + - + +
411A ARG* 2.9 39.7 + - + +
414A LYS* 3.5 12.6 + - - +
415A MET* 3.6 35.7 - - + -
416A PRO* 3.7 22.4 - - + -
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Residues in contact with CYS 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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311A HIS 3.1 21.1 + - - -
312A LEU* 3.8 10.1 - - - +
313A ARG 3.2 0.2 - - - -
314A TYR* 1.3 75.2 - - - +
316A ASP* 1.3 60.1 + - - +
318A ILE* 3.1 9.4 + - - +
319A LEU* 2.9 24.6 + - - +
365A MET* 4.1 4.0 - - + -
373A ALA* 3.9 25.4 - - - -
376A PHE* 3.5 51.5 - - + -
412A PHE* 4.3 10.1 - - - -
415A MET* 4.6 3.6 - - - -
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Residues in contact with ASP 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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308A LEU* 4.6 8.5 - - + +
312A LEU 3.3 10.9 + - - +
313A ARG* 3.3 12.9 + - + +
315A CYS* 1.3 79.1 - - - +
317A SER* 1.3 57.3 + - - +
319A LEU* 3.8 14.2 - - - +
320A ARG* 3.0 43.7 + - - +
362A LYS* 5.9 1.0 - - - +
365A MET* 3.3 30.6 - - + +
366A ASP* 4.8 7.8 - - - +
368A ARG* 5.5 1.6 + - - -
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Residues in contact with SER 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 ARG 3.1 12.4 + - - -
314A TYR* 3.2 19.6 - - - -
315A CYS 3.1 0.2 - - - -
316A ASP* 1.3 75.4 - - - +
318A ILE* 1.3 64.3 + - - +
320A ARG* 3.3 28.9 + - - +
321A GLU* 3.1 21.9 + - - +
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Residues in contact with ILE 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 TYR* 3.1 43.6 + - + +
315A CYS* 3.5 11.9 - - - +
317A SER* 1.3 73.7 - - - +
319A LEU* 1.3 59.5 + - - +
321A GLU* 3.0 11.8 + - + +
322A MET* 2.9 44.8 + - + +
376A PHE* 4.8 4.7 - - + -
407A VAL* 5.6 0.7 - - + -
408A PHE* 4.1 17.3 - - + -
411A ARG* 3.7 35.0 - - + +
412A PHE* 3.7 23.8 - - + +
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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
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315A CYS 2.9 16.6 + - - +
316A ASP* 3.8 21.3 - - - +
318A ILE* 1.3 76.0 - - - +
320A ARG* 1.3 62.9 + - - +
322A MET* 3.3 11.9 + - + +
323A LEU* 3.2 34.5 + - + +
358A LEU* 3.9 37.0 - - + +
361A VAL* 4.0 18.2 - - + +
362A LYS* 3.6 33.9 - - + +
365A MET* 4.4 5.4 - - + -
376A PHE* 4.2 8.9 - - + -
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Residues in contact with ARG 320 (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 ARG 5.5 0.6 + - - -
316A ASP* 3.0 47.1 + - - +
317A SER* 3.5 29.0 + - - +
318A ILE 3.2 0.2 - - - -
319A LEU* 1.3 78.0 - - - +
321A GLU* 1.3 59.8 + - - +
323A LEU* 3.6 8.6 + - - +
324A SER* 3.5 19.4 + - - -
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Residues in contact with GLU 321 (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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317A SER* 3.1 12.7 + - - +
318A ILE* 3.0 11.3 + - - +
320A ARG* 1.3 75.6 - - - +
322A MET* 1.3 63.7 + - + +
323A LEU 3.1 1.8 - - - -
324A SER* 2.5 29.2 + - - +
326A LYS* 4.7 8.8 - - + +
327A HIS* 3.1 34.2 + - + +
407A VAL* 4.0 6.0 - - + +
411A ARG* 2.5 54.2 + - - +
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Residues in contact with MET 322 (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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318A ILE* 2.9 25.7 + - + +
319A LEU* 3.3 28.4 + - + +
321A GLU* 1.3 75.6 - - - +
323A LEU* 1.3 59.3 + - - +
324A SER 3.4 2.1 + - - +
327A HIS* 4.4 7.2 - - - +
331A ALA* 3.5 26.7 - - - +
335A TYR* 4.1 0.5 - - - -
358A LEU* 4.0 33.3 - - + +
376A PHE* 4.5 6.1 - - + -
380A VAL* 4.4 12.1 - - + -
384A PHE* 5.0 2.0 - - - -
404A LEU* 3.9 27.6 - - + -
407A VAL* 4.8 10.8 - - + -
408A PHE* 4.0 31.6 - - + -
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Residues in contact with LEU 323 (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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319A LEU* 3.2 34.9 + - + +
320A ARG* 3.6 8.0 + - - +
321A GLU 3.1 0.8 - - - -
322A MET* 1.3 76.7 - - - +
324A SER* 1.3 63.6 + - - +
335A TYR* 3.7 34.8 + - + +
358A LEU* 3.7 37.0 - - + +
359A SER* 5.3 1.3 - - - +
362A LYS* 4.5 20.2 - - + -
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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