Contacts of the helix formed by residues 315 - 327 (chain A) in PDB entry 1LWZ
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 ALA 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 LYS 3.5 2.7 + - - -
314A VAL* 1.3 72.1 - - - +
316A GLN* 1.3 60.5 + - - +
318A ALA* 3.3 8.1 + - - +
319A GLY* 3.1 19.9 + - - -
336A MET* 3.1 34.9 - - + +
339A ILE* 4.6 18.0 - - + +
343A GLN* 5.6 0.4 - - - +
374A ARG* 3.3 13.9 + - - +
377A PHE* 3.0 20.9 + - + +
378A THR* 4.3 0.4 - - - +
379A MET* 5.1 5.2 - - + -
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Residues in contact with GLN 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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218A ALA* 4.0 12.1 - - + -
242A ARG* 5.7 8.5 + - - +
244A GLN* 4.7 12.6 - - - +
314A VAL* 3.7 9.2 - - + +
315A ALA* 1.3 79.8 - - - +
317A LEU* 1.3 72.4 + - - +
319A GLY 3.8 0.5 + - - -
320A SER* 4.0 13.7 + - - -
332A MET* 4.6 6.9 - - + +
374A ARG* 2.9 52.0 + - + +
375A TYR* 3.7 17.7 - - + -
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Residues in contact with LEU 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 LYS* 3.9 31.4 - - + -
314A VAL* 2.8 25.6 - - + +
316A GLN* 1.3 85.8 + - - +
318A ALA* 1.4 64.3 + - - +
319A GLY 3.4 0.3 + - - -
320A SER* 3.6 11.5 + - - -
321A VAL* 3.5 19.7 + - + +
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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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300A LEU* 5.3 0.7 - - + -
309A LYS* 3.7 16.9 + - - +
313A LYS* 3.3 29.6 - - + +
314A VAL 2.9 11.4 + - - +
315A ALA* 3.3 8.5 + - - +
317A LEU* 1.4 73.8 - - - +
319A GLY* 1.3 65.6 + - - +
321A VAL* 3.1 6.3 + - - +
322A ALA* 3.0 22.5 + - - +
335A MET* 4.2 1.8 - - + -
339A ILE* 4.9 4.9 - - + -
379A MET* 4.4 15.0 - - + -
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Residues in contact with GLY 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 ALA 3.1 10.0 + - - -
317A LEU 3.3 0.4 - - - -
318A ALA* 1.3 76.2 - - - +
320A SER* 1.3 62.6 + - - +
322A ALA 3.2 1.4 + - - -
323A GLU* 2.9 23.6 + - - +
332A MET* 4.0 5.4 - - - -
335A MET* 2.9 25.7 - - - +
374A ARG* 3.1 21.7 - - - +
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Residues in contact with SER 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A GLN* 4.0 10.1 + - - -
317A LEU* 3.6 9.4 + - - -
318A ALA 3.4 0.4 - - - -
319A GLY* 1.3 74.9 - - - +
321A VAL* 1.3 62.9 + - - +
323A GLU* 2.7 39.6 + - - +
324A MET* 3.0 10.6 + - - +
332A MET* 3.8 17.5 - - - +
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Residues in contact with VAL 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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303A CYS* 3.7 7.2 - - - -
307A ASN* 2.9 33.7 - - - +
309A LYS* 5.3 4.0 - - - +
313A LYS* 5.0 9.6 - - - -
317A LEU* 3.5 22.4 - - + +
318A ALA* 3.1 10.7 + - - +
320A SER* 1.3 78.1 - - - +
322A ALA* 1.3 62.1 + - - +
324A MET* 3.3 12.9 + - + +
325A SER* 3.1 22.8 + - - -
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Residues in contact with ALA 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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299A VAL* 4.8 2.0 - - + +
300A LEU* 4.2 9.4 - - + -
303A CYS* 3.1 32.0 - - + +
318A ALA 3.0 7.9 + - - +
321A VAL* 1.3 75.7 - - - +
323A GLU* 1.3 54.9 + - - +
325A SER* 3.9 0.9 - - - -
326A SER* 2.6 41.7 + - - +
335A MET* 3.1 34.8 - - + -
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Residues in contact with GLU 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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256A TYR* 5.8 0.3 - - - -
319A GLY 2.9 9.3 + - - +
320A SER* 2.7 35.5 + - - +
322A ALA* 1.3 77.4 - - - +
324A MET* 1.3 58.0 + - + +
326A SER* 3.7 6.3 - - - -
327A TYR* 2.8 28.2 + - - -
328A HIS* 3.4 25.6 + - + +
330A GLY 4.7 4.3 - - - +
332A MET* 3.1 44.5 - - + +
335A MET* 4.7 4.7 - - + +
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Residues in contact with MET 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 SER 3.0 17.1 + - - +
321A VAL* 3.3 11.2 + - + +
323A GLU* 1.3 82.3 - - + +
325A SER* 1.3 67.2 + - - +
327A TYR* 3.6 4.0 + - - -
405A ARG* 3.1 36.5 + - - +
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Residues in contact with SER 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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302A THR* 6.0 1.4 - - - +
303A CYS* 4.9 12.3 - - - -
306A ARG* 4.5 21.6 + - - +
307A ASN* 5.6 2.2 - - - -
321A VAL* 3.1 16.6 + - - -
322A ALA 4.1 2.7 - - - -
324A MET* 1.3 84.7 - - - +
326A SER* 1.3 58.4 + - - +
327A TYR* 3.5 0.7 + - - +
405A ARG* 5.2 7.7 - - - +
406A VAL 4.1 15.8 + - - +
407A GLU* 4.6 3.6 - - - +
408A PRO* 5.1 0.7 - - - +
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Residues in contact with SER 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A VAL* 3.5 39.1 - - - +
302A THR* 5.1 1.6 - - - -
303A CYS* 5.9 0.4 - - - -
322A ALA 2.6 26.4 + - - -
325A SER* 1.3 78.6 - - - +
327A TYR* 1.3 71.2 + - - +
328A HIS* 3.3 17.3 + - - +
407A GLU* 3.3 18.4 - - - +
408A PRO* 4.2 13.9 - - - +
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Residues in contact with TYR 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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179A LYS* 6.0 1.0 - - - +
255A LEU* 4.6 11.1 - - + +
323A GLU 2.8 14.0 + - - -
324A MET 3.6 4.9 + - - +
325A SER 3.5 2.8 - - - +
326A SER* 1.3 75.5 - - - +
328A HIS* 1.4 64.7 + - - +
329A HIS* 2.8 40.6 + + - -
402A ASP* 3.6 20.2 - - + +
403A ASN* 3.7 25.7 + - + -
405A ARG* 5.1 20.2 - - + +
407A GLU* 3.2 13.8 - - + +
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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