Contacts of the helix formed by residues 313 - 321 (chain A) in PDB entry 3LX9
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 313 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A ALA 3.1 12.8 + - - +
310A LEU* 3.1 21.1 + - + +
311A LEU 3.4 1.2 - - - -
312A GLN* 1.3 72.9 - - - +
314A LYS* 1.3 58.5 + - - +
315A ASP* 3.1 14.7 + - - +
316A VAL* 3.1 37.4 + - + +
317A ILE* 2.9 31.4 + - - +
387A LEU* 4.5 5.1 - - - +
388A LEU* 3.9 14.6 - - - +
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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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312A GLN 2.9 9.4 + - - +
313A ASP* 1.3 72.3 + - - +
315A ASP* 1.3 64.3 + - - +
317A ILE* 3.6 6.8 + - - +
318A ALA* 2.9 30.6 + - + +
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Residues in contact with ASP 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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313A ASP* 3.1 9.3 + - - +
314A LYS* 1.3 81.0 - - - +
316A VAL* 1.3 64.7 + - - +
318A ALA* 3.4 8.6 + - - +
319A ILE* 3.2 25.6 + - - +
387A LEU* 3.7 27.1 - - + +
391A LYS* 2.8 41.6 + - - +
416A GLN* 4.5 4.0 - - - +
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Residues in contact with VAL 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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284A MET* 3.8 32.5 - - + +
288A ALA* 3.7 23.0 - - + +
313A ASP* 3.1 31.8 + - + +
315A ASP* 1.3 73.3 - - - +
317A ILE* 1.3 66.0 + - - +
319A ILE* 3.1 10.6 + - - +
320A ASN* 3.1 18.4 + - - +
387A LEU* 4.5 7.4 - - + -
388A LEU* 3.8 26.5 - - + -
414A LEU* 3.9 15.7 - - + -
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Residues in contact with ILE 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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42A MET* 3.9 29.6 - - + -
84A ALA* 3.7 33.0 - - + +
86A TYR* 4.6 0.2 - - - +
284A MET* 4.1 10.8 - - + -
294A LEU* 4.7 3.6 - - + -
311A LEU 3.4 26.0 - - - +
312A GLN* 3.7 15.7 - - - +
313A ASP 2.9 20.9 + - - +
314A LYS* 3.9 6.1 - - - +
316A VAL* 1.3 75.8 - - - +
318A ALA* 1.3 53.9 + - - +
320A ASN* 3.2 7.0 + - - +
321A GLN* 2.8 40.0 + - + +
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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 21.4 + - + +
315A ASP* 3.5 9.9 - - - +
316A VAL 3.2 0.2 - - - -
317A ILE* 1.3 78.1 - - - +
319A ILE* 1.3 61.0 + - + +
321A GLN* 3.6 5.5 + - - -
322A ASP* 3.1 23.0 + - - +
416A GLN* 6.1 0.4 - - - +
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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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288A ALA* 4.0 20.9 - - + +
289A ILE* 4.7 1.1 - - + +
315A ASP 3.2 11.2 + - - +
316A VAL* 3.1 8.1 + - - +
318A ALA* 1.3 73.5 - - - +
320A ASN* 1.3 66.1 + - - +
322A ASP* 3.1 14.7 + - - +
342A ARG* 2.9 16.4 + - - -
344A LEU* 3.9 21.8 - - + -
350A ALA* 3.7 34.1 - - + -
387A LEU* 3.5 28.3 - - + -
414A LEU* 4.0 18.4 - - + -
416A GLN* 3.7 16.8 - - + +
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Residues in contact with ASN 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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40A PRO* 3.6 15.7 - - - +
287A TRP 3.1 21.2 + - - -
288A ALA* 3.7 12.7 - - + +
291A ALA 3.9 1.2 - - - -
292A ALA 2.8 31.5 + - - +
294A LEU* 3.5 31.4 - - + +
316A VAL 3.1 7.9 + - - +
317A ILE 3.2 7.2 + - - +
319A ILE* 1.3 78.6 - - - +
321A GLN* 1.3 86.1 + - - +
322A ASP 3.4 2.3 + - - -
342A ARG* 3.2 20.5 + - - +
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Residues in contact with GLN 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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39A THR* 2.6 40.7 + - + +
40A PRO* 2.7 33.3 + - - +
42A MET* 3.6 29.6 - - - +
317A ILE* 2.8 28.6 + - + +
318A ALA* 3.6 6.1 - - - +
320A ASN* 1.3 93.2 + - - +
322A ASP* 1.3 66.0 + - - +
323A PRO* 3.2 5.7 - - - +
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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