Contacts of the helix formed by residues 308 - 322 (chain A) in PDB entry 1LMU
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 308 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298A GLN 5.9 0.2 - - - -
306A GLY 3.9 2.4 + - - -
307A LEU* 1.3 76.4 - - - +
309A ALA* 1.3 74.4 + - - +
310A GLN 3.2 8.2 + - - -
311A ASN* 3.2 16.4 + - - +
312A VAL* 3.0 21.7 + - - +
493A ASP* 4.0 19.4 + - - -
532A ILE* 5.7 4.7 - - - +
533A GLU* 3.5 17.9 + - - -
543A LYS* 5.6 3.1 - - - -
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Residues in contact with ALA 309 (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 GLN* 3.3 35.7 + - + +
302A ALA* 6.0 0.4 - - - +
308A SER* 1.3 77.0 + - - +
310A GLN* 1.3 61.4 + - - +
312A VAL* 3.0 25.2 - - - +
313A LEU* 3.0 4.7 + - - +
493A ASP* 5.3 4.9 - - - +
497A LEU* 4.3 15.0 - - + -
529A ALA* 3.6 17.9 - - + -
532A ILE* 4.3 10.7 - - + +
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Residues in contact with GLN 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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308A SER* 3.2 1.6 + - - +
309A ALA* 1.3 79.6 - - - +
311A ASN* 1.3 64.9 + - - +
313A LEU* 3.1 14.0 + - + +
314A ASP* 2.5 61.1 + - - +
529A ALA* 3.6 15.8 - - + +
530A GLY* 5.5 1.3 - - - +
533A GLU* 3.3 41.3 - - + +
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Residues in contact with ASN 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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307A LEU* 3.6 26.7 - - + +
308A SER* 3.2 27.3 + - - +
310A GLN* 1.3 84.8 + - - +
312A VAL* 1.3 61.0 + - - +
314A ASP* 3.1 9.0 + - - +
315A ILE* 3.0 35.5 + - - +
398A ASN* 4.7 6.2 + - - +
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Residues in contact with VAL 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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294A LEU* 4.5 4.3 - - + -
297A LEU* 3.9 20.9 - - + -
298A GLN* 3.2 33.4 - - + +
301A ALA* 4.0 19.7 - - + -
307A LEU* 4.8 3.8 - - + +
308A SER 3.0 11.7 + - - +
309A ALA 3.0 15.9 - - - +
311A ASN* 1.3 73.4 - - - +
313A LEU* 1.3 70.5 + - - +
315A ILE* 3.3 5.2 + - - +
316A CYS* 2.9 30.1 + - - -
402A VAL* 3.6 27.8 - - + -
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Residues in contact with LEU 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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294A LEU* 3.7 30.1 - - + -
298A GLN* 4.7 4.9 - - - +
309A ALA 3.0 8.6 + - - +
310A GLN* 3.1 21.1 + - + +
312A VAL* 1.3 84.3 - - - +
314A ASP* 1.3 63.7 + - - +
316A CYS* 3.3 8.7 + - + +
317A GLN* 3.1 29.7 + - + +
329A PRO* 5.0 2.2 - - + +
330A ARG* 4.2 39.9 - - + +
526A ALA* 4.6 14.4 - - - +
529A ALA* 4.9 9.6 - - + -
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Residues in contact with ASP 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 GLN* 2.5 50.4 + - - +
311A ASN* 3.1 14.2 + - - +
313A LEU* 1.3 78.4 - - - +
315A ILE* 1.3 63.9 + - + +
317A GLN* 3.1 18.4 + - - +
318A LYS* 3.2 12.0 + - - +
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Residues in contact with ILE 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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307A LEU* 4.9 3.1 - - + -
311A ASN* 3.0 32.2 + - - +
312A VAL* 3.3 8.3 + - - +
314A ASP* 1.3 76.7 - - + +
316A CYS* 1.3 62.5 + - - +
318A LYS* 3.0 10.1 + - + +
319A LEU* 3.0 20.5 + - + +
398A ASN* 3.9 26.5 - - + +
399A GLU* 3.7 21.3 - - + +
402A VAL* 3.0 43.1 - - + -
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Residues in contact with CYS 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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294A LEU* 4.3 10.3 - - + -
297A LEU* 3.5 32.5 - - - -
312A VAL* 2.9 29.5 + - - +
313A LEU* 3.5 7.0 - - - +
314A ASP 3.2 0.2 - - - -
315A ILE* 1.3 78.1 - - - +
317A GLN* 1.3 62.6 + - - +
319A LEU* 3.3 8.9 + - - +
320A TYR* 2.9 26.0 + - - +
326A ILE* 3.8 4.0 - - + +
329A PRO* 3.4 26.2 - - + +
384A ILE* 5.3 2.2 - - - -
402A VAL* 5.5 2.5 - - - -
406A ILE* 5.1 7.0 - - - -
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Residues in contact with GLN 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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8A LYS* 5.3 1.8 - - - +
313A LEU* 3.1 24.1 + - + +
314A ASP* 3.1 11.4 + - - +
316A CYS* 1.3 75.9 - - - +
318A LYS* 1.3 55.3 + - - +
320A TYR* 4.3 7.4 - - - -
321A GLU* 2.7 74.2 + - - +
328A TYR* 5.5 3.1 - - - -
329A PRO* 3.9 16.0 - - + +
330A ARG* 3.5 40.4 + - - +
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Residues in contact with LYS 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 ASP 3.2 7.7 + - - +
315A ILE* 3.0 13.9 + - + +
317A GLN* 1.3 79.2 - - - +
319A LEU* 1.3 59.7 + - + +
321A GLU* 5.4 0.2 - - - -
322A THR* 2.9 46.9 + - - +
323A HIS* 3.1 32.0 + - + -
396A THR* 3.9 9.3 + - - -
399A GLU* 3.0 30.7 + - - +
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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 ILE* 3.0 19.0 + - + +
316A CYS* 3.8 5.2 - - - +
318A LYS* 1.3 76.3 - - - +
320A TYR* 1.3 51.7 + - - +
323A HIS* 3.5 11.0 - - + +
324A LYS 2.8 28.9 + - - -
325A LEU* 3.0 35.2 + - + -
326A ILE* 2.9 17.9 - - + -
395A LEU* 3.4 23.3 - - + -
399A GLU* 3.5 19.1 - - + +
402A VAL* 3.4 30.7 - - + -
403A TYR* 4.0 11.9 - - + +
406A ILE* 4.5 11.4 - - + -
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Residues in contact with TYR 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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8A LYS* 4.8 8.7 + - - -
11A LEU* 5.3 3.0 - - + +
103A ASP* 5.2 2.3 + - - -
134A ILE* 3.7 24.4 + - - +
135A ASN 3.2 24.1 + - - -
137A LEU* 2.9 48.8 - - + +
316A CYS 2.9 15.5 + - - +
317A GLN* 3.6 5.8 - - - +
319A LEU* 1.3 76.2 - - - +
321A GLU* 1.4 82.4 + - + +
324A LYS* 3.2 14.2 - - - -
326A ILE* 2.8 30.1 - - + +
327A THR 3.4 9.6 - - - -
328A TYR* 3.2 26.9 - + - -
329A PRO* 3.4 18.4 - - + -
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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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8A LYS* 3.5 22.5 + - - +
10A SER* 2.7 39.2 + - - +
137A LEU* 4.1 9.5 - - + +
317A GLN* 2.7 44.8 + - - +
318A LYS* 5.4 0.2 - - - -
320A TYR* 1.4 95.7 - - + +
322A THR* 1.4 66.8 + - - +
324A LYS* 3.7 16.1 - - - +
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Residues in contact with THR 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 LYS* 2.9 37.4 + - + +
321A GLU* 1.4 79.0 - - - +
323A HIS* 1.3 75.5 + - + +
324A LYS* 4.0 9.0 - - - +
389A ARG* 5.8 0.7 - - - -
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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