Contacts of the helix formed by residues 314 - 324 (chain A) in PDB entry 5JXL
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 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289A TRP* 3.2 11.8 + - - -
290A GLY 4.7 0.4 - - - -
312A ILE* 3.5 8.3 - - - +
313A ARG* 1.3 81.0 - - - +
315A LEU* 1.3 66.1 + - - +
316A ASP* 2.3 34.2 + - - -
317A GLU* 3.0 26.6 + - - +
318A ALA 3.5 0.3 + - - -
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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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289A TRP* 3.5 55.1 + - + +
314A SER* 1.3 74.4 - - - +
316A ASP* 1.3 66.9 + - + +
318A ALA* 2.9 21.5 + - - +
319A ILE* 2.9 25.5 + - + +
341A LYS* 3.4 40.8 - - + +
345A GLY 3.6 25.8 - - - +
346A SER 5.1 0.2 - - - +
347A GLY 4.9 7.9 - - - +
348A ILE* 6.2 1.1 - - + -
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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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314A SER* 2.3 31.0 + - - -
315A LEU* 1.3 86.5 - - + +
317A GLU* 1.3 79.3 + - - +
319A ILE* 3.0 13.8 + - + +
320A ALA* 2.9 28.1 + - - +
341A LYS* 6.0 3.1 - - + -
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Residues in contact with GLU 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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311A ASN 3.8 4.0 - - - +
312A ILE* 3.6 15.2 - - + +
313A ARG* 2.9 42.6 + - - +
314A SER* 3.0 10.1 + - - +
316A ASP* 1.3 92.0 + - - +
318A ALA* 1.3 60.7 + - - +
320A ALA* 3.8 5.8 - - - +
321A TYR* 2.9 31.7 + - - +
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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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289A TRP* 4.3 16.8 - - + -
298A LEU* 3.7 30.3 - - + -
312A ILE* 4.4 7.7 - - + +
314A SER 3.5 3.5 + - - +
315A LEU* 2.9 16.0 + - - +
317A GLU* 1.3 78.4 - - - +
319A ILE* 1.3 58.0 + - + +
321A TYR* 4.0 1.7 - - - +
322A ILE* 2.9 44.5 + - + +
348A ILE* 5.2 0.9 - - + -
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Residues in contact with ILE 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 LEU* 2.9 25.3 + - + +
316A ASP* 3.0 14.6 + - + +
318A ALA* 1.3 78.3 - - - +
320A ALA* 1.3 57.5 + - - +
322A ILE* 3.7 3.8 - - - +
323A ASN* 2.9 49.0 + - - +
339A ALA* 4.1 17.4 - - + +
340A VAL* 4.4 9.2 - - - +
341A LYS* 4.4 17.7 - - + +
347A GLY 5.1 0.2 - - - +
348A ILE* 3.5 41.7 - - + -
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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
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316A ASP 2.9 14.8 + - - +
317A GLU* 3.8 6.1 - - - +
319A ILE* 1.3 77.8 - - - +
321A TYR* 1.3 59.0 + - - +
323A ASN* 2.8 26.4 + - - +
324A THR* 2.9 17.7 + - + +
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Residues in contact with TYR 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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298A LEU* 4.6 4.9 - - + -
307A ILE* 3.4 31.9 - - + -
308A GLN 2.7 28.4 + - - -
309A ASN* 3.9 27.1 - - + +
312A ILE* 5.3 2.0 - - + -
317A GLU 2.9 18.6 + - - +
318A ALA* 4.0 4.3 - - - +
320A ALA* 1.3 76.8 - - - +
322A ILE* 1.3 57.7 + - - +
324A THR* 2.3 36.5 + - + -
325A PHE* 3.1 33.8 - + - -
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Residues in contact with ILE 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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298A LEU* 5.6 4.7 - - + -
300A ILE* 5.8 7.9 - - + -
302A LEU* 4.7 13.7 - - + -
307A ILE* 4.6 21.8 - - + -
318A ALA* 2.9 31.3 + - + +
319A ILE* 3.7 3.8 - - - +
321A TYR* 1.3 77.9 - - + +
323A ASN* 1.3 62.6 + - - +
324A THR 3.1 0.2 - - - -
325A PHE* 3.1 24.0 + - - +
326A THR* 4.1 2.4 + - - -
335A THR* 5.5 0.5 + - - -
337A VAL* 5.2 6.3 - - + +
339A ALA* 3.9 22.2 - - + +
348A ILE* 4.0 26.7 - - + -
350A PHE* 4.6 18.6 - - + -
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Residues in contact with ASN 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 ILE* 2.9 38.1 + - - +
320A ALA* 2.8 14.0 + - - +
322A ILE* 1.3 77.7 - - - +
324A THR* 1.3 61.4 + - + +
325A PHE 3.1 0.2 - - - -
326A THR* 3.1 27.7 - - - +
337A VAL 5.6 0.9 - - - -
338A LYS* 3.6 23.3 - - + +
339A ALA* 3.3 35.1 + - - +
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Residues in contact with THR 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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320A ALA* 2.9 15.0 + - + +
321A TYR* 2.3 39.4 + - + +
323A ASN* 1.3 78.9 - - - +
325A PHE* 1.3 68.6 + - - +
326A THR* 3.3 2.1 + - - +
327A ALA* 4.4 6.2 + - - +
332A ARG* 3.9 14.9 + - - -
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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