Contacts of the helix formed by residues 315 - 327 (chain A) in PDB entry 1JSC
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 ASP 315 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A HIS* 3.1 22.5 + - + +
314A ALA* 1.3 80.6 - - - +
316A GLY* 1.3 65.6 + - - +
317A PRO 3.4 2.2 - - - -
318A ARG* 3.0 41.2 + - - +
319A LEU* 3.0 25.6 + - + +
428A THR* 3.8 9.0 - - + -
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Residues in contact with GLY 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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310A ILE* 3.5 25.6 - - - +
313A HIS 3.2 5.1 + - - -
315A ASP* 1.3 75.8 - - - +
317A PRO* 1.3 70.9 - - - +
319A LEU* 3.2 2.0 + - - +
320A LEU* 2.9 19.2 + - - +
428A THR* 3.1 29.3 - - - +
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Residues in contact with PRO 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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310A ILE* 3.6 12.6 - - + +
311A LEU* 4.0 12.8 - - + -
313A HIS 3.9 6.5 - - - +
314A ALA 4.0 7.2 - - - +
315A ASP 3.8 2.2 - - - -
316A GLY* 1.3 88.4 - - - +
318A ARG* 1.3 60.7 - - - +
320A LEU* 3.4 6.7 + - + +
321A LYS* 3.1 22.0 + - - +
340A SER* 3.6 27.6 - - - +
341A PHE* 5.9 0.3 - - - -
513A PRO* 3.6 36.8 - - + -
514A HIS* 5.5 2.5 - - + +
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Residues in contact with ARG 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 ALA 5.2 0.9 + - - +
315A ASP* 3.0 41.5 + - - +
317A PRO* 1.3 79.4 - - - +
319A LEU* 1.3 74.3 + - - +
321A LYS* 3.3 7.5 + - - +
322A GLU* 3.0 47.7 + - + +
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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 ASP* 3.0 19.7 + - + +
316A GLY* 3.8 4.0 - - - +
318A ARG* 1.3 96.8 - - - +
320A LEU* 1.3 66.0 + - - +
322A GLU* 3.2 26.4 + - + +
323A LEU* 2.9 23.9 + - - +
428A THR* 3.4 35.7 - - + +
431A LEU* 4.3 16.0 - - + +
432A GLY* 3.7 21.8 - - - +
435A MET* 4.5 10.2 - - + +
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Residues in contact with LEU 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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304A LEU* 3.8 26.7 - - + -
306A VAL* 3.7 45.3 - - + -
310A ILE* 4.5 10.5 - - + -
316A GLY 2.9 16.3 + - - +
317A PRO* 3.6 5.6 - - + +
319A LEU* 1.3 76.8 - - - +
321A LYS* 1.3 63.8 + - - +
323A LEU* 3.2 4.9 + - + +
324A SER* 2.9 22.0 + - - -
331A VAL* 4.6 2.7 - - + -
340A SER* 4.2 22.4 - - - +
341A PHE* 4.4 19.1 - - + -
373A VAL* 5.4 2.5 - - + -
431A LEU* 4.6 13.8 - - + +
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Residues in contact with LYS 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 PRO 3.1 10.5 + - - +
318A ARG* 3.3 9.8 + - - +
320A LEU* 1.3 78.4 - - - +
322A GLU* 1.3 63.6 + - - +
324A SER* 3.2 5.8 + - - -
325A ASP* 2.7 64.2 + - - +
341A PHE* 4.3 19.5 - - + -
342A ASP* 6.5 1.1 - - - -
345A ASP* 3.6 17.8 + - - -
347A LYS* 4.8 0.2 - - - +
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Residues in contact with GLU 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 ARG* 3.0 25.5 + - + +
319A LEU* 3.4 28.6 - - - +
320A LEU 3.2 0.2 - - - -
321A LYS* 1.3 78.0 - - - +
323A LEU* 1.3 57.6 + - - +
325A ASP* 3.3 5.8 + - - +
326A ARG* 2.9 34.8 + - + +
435A MET* 3.0 34.4 - - + +
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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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296A ILE* 4.8 15.0 - - + -
304A LEU* 4.3 22.7 - - + -
319A LEU 2.9 16.9 + - - +
320A LEU* 3.7 4.9 - - + +
322A GLU* 1.3 72.5 - - - +
324A SER* 1.3 65.6 + - - +
326A ARG* 4.5 1.3 - - - -
327A ALA* 3.2 23.0 + - - +
329A ILE* 4.2 16.6 - - + +
371A ILE* 5.3 1.6 - - + -
431A LEU* 4.0 30.7 - - + -
434A MET* 5.4 2.0 - - - -
435A MET* 4.0 16.4 - - - -
438A ILE* 4.0 39.0 - - + -
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Residues in contact with SER 324 (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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304A LEU* 4.3 6.2 - - - +
320A LEU 2.9 17.0 + - - -
321A LYS 3.6 4.5 - - - -
323A LEU* 1.3 77.3 - - - +
325A ASP* 1.3 57.5 + - - +
328A GLN* 3.0 9.4 + - - -
329A ILE* 2.8 49.0 + - - +
331A VAL* 3.7 19.0 - - - +
341A PHE* 3.9 12.5 - - - -
347A LYS* 3.2 18.2 - - - +
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Residues in contact with ASP 325 (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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321A LYS* 2.7 55.4 + - - +
322A GLU* 3.8 5.1 + - - +
324A SER* 1.3 75.7 - - - +
326A ARG* 1.3 66.3 + - - +
328A GLN* 2.7 27.2 + - - +
347A LYS* 2.7 31.7 + - - -
441A VAL 4.6 1.0 - - - +
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Residues in contact with ARG 326 (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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322A GLU* 2.9 21.5 + - + +
323A LEU* 4.0 3.4 - - - +
325A ASP* 1.3 79.7 - - - +
327A ALA* 1.3 58.4 + - - +
435A MET* 3.1 48.9 + - + +
436A SER* 3.5 19.4 + - - +
438A ILE* 2.8 37.7 + - + -
440A PRO* 3.3 29.9 - - + +
441A VAL 2.8 26.5 + - - +
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Residues in contact with ALA 327 (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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296A ILE* 4.5 4.7 - - + -
323A LEU* 3.2 7.4 + - + +
326A ARG* 1.3 77.7 - - - +
328A GLN* 1.3 69.1 + - - +
329A ILE* 3.3 25.1 + - + +
438A ILE* 3.8 22.7 - - + -
439A PHE 4.4 4.0 - - - +
441A VAL* 3.9 10.2 - - + +
444A ARG* 2.8 33.3 + - - +
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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