Contacts of the helix formed by residues 303 - 319 (chain A) in PDB entry 3LJK
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 ASN 303 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 4.0 1.9 - - - +
294A HIS* 3.7 7.6 + - - -
295A PHE* 2.9 39.2 + - - +
298A THR* 3.0 18.5 + - + +
299A GLU 3.4 13.5 - - - +
300A PHE* 3.2 17.0 + - - +
301A SER 3.6 0.4 - - - -
302A LYS* 1.3 74.8 - - - +
304A ILE* 1.3 62.9 + - - +
305A PRO* 3.2 18.7 - - - +
306A VAL* 3.2 23.5 + - + +
307A ILE* 3.0 23.2 + - - +
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Residues in contact with ILE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 3.7 33.4 - - + -
35A LYS 4.4 0.4 - - - -
36A HIS* 3.9 34.1 - - + +
39A ILE* 5.1 6.1 - - + -
41A PHE* 3.7 42.8 - - + -
294A HIS* 3.0 19.8 - - + +
303A ASN* 1.3 69.9 - - - +
305A PRO* 1.4 68.8 - - + +
307A ILE* 3.2 4.1 + - - +
308A MSE 2.9 38.8 + - - +
479A LEU* 3.9 18.6 - - + -
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Residues in contact with PRO 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A VAL* 4.7 2.5 - - + -
294A HIS* 3.9 10.1 - - - +
295A PHE* 4.0 14.8 - - + -
303A ASN* 3.2 12.1 - - - +
304A ILE* 1.4 94.6 - - + +
306A VAL* 1.3 55.9 + - - +
308A MSE 3.4 13.4 + - + +
309A ALA* 3.0 29.8 + - - +
479A LEU* 3.8 22.4 - - + +
482A HIS* 3.6 32.5 - - + -
483A LYS* 3.7 12.8 - - - +
486A VAL* 4.6 1.3 - - - -
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Residues in contact with VAL 306 (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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60A ALA* 4.3 2.7 - - + -
65A LEU* 4.1 16.4 - - + -
295A PHE* 3.9 16.4 - - + -
300A PHE* 4.0 33.2 - - + +
303A ASN* 3.2 36.2 + - + +
304A ILE 3.2 1.0 - - - -
305A PRO* 1.3 77.3 - - - +
307A ILE* 1.3 56.7 + - - +
309A ALA* 3.3 1.9 + - - +
310A LEU* 2.9 48.4 + - + +
486A VAL* 4.1 13.2 - - + -
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Residues in contact with ILE 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 4.3 15.0 - - + -
41A PHE* 3.9 17.7 - - + -
43A TYR* 3.8 33.4 - - + +
53A LEU* 4.0 24.5 - - + -
57A LEU* 4.1 13.0 - - + -
300A PHE 4.0 16.2 - - - +
301A SER* 4.3 6.7 - - - +
303A ASN 3.0 14.7 + - - +
304A ILE* 3.7 5.4 - - - +
306A VAL* 1.3 76.4 - - - +
308A MSE 1.3 63.5 + - - +
310A LEU* 3.3 6.0 + - + +
311A LEU* 3.0 35.5 + - + +
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Residues in contact with MSE 308 (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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41A PHE* 3.5 25.4 - - + -
304A ILE* 2.9 35.5 + - - +
305A PRO* 3.6 13.0 - - - +
307A ILE* 1.3 75.2 - - - +
309A ALA* 1.3 62.9 + - - +
311A LEU* 3.5 5.9 + - - +
312A ALA* 3.1 25.5 + - - +
393A ASP* 4.6 4.0 - - - +
463A ILE* 4.3 8.5 - - + -
479A LEU* 4.1 18.6 - - + +
480A TYR* 3.4 52.7 - - + +
483A LYS* 3.8 21.9 - - + -
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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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305A PRO 3.0 15.9 + - - +
306A VAL 3.6 0.7 - - - +
308A MSE 1.3 74.9 - - - +
310A LEU* 1.3 65.6 + - - +
312A ALA* 3.3 1.2 + - - +
313A SER* 2.9 30.6 + - - -
483A LYS* 3.5 16.4 - - - +
486A VAL* 3.3 37.2 - - + -
487A GLN* 3.7 14.4 - - + -
490A LEU* 5.0 1.8 - - + -
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Residues in contact with LEU 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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3A PHE* 4.0 16.3 - - + -
53A LEU* 5.6 2.7 - - + -
56A LEU* 3.5 45.1 - - + +
57A LEU* 3.9 22.2 - - + +
60A ALA* 4.1 9.6 - - + +
306A VAL* 2.9 38.2 + - + +
307A ILE* 3.9 8.5 - - + +
309A ALA* 1.3 75.1 - - - +
311A LEU* 1.3 58.8 + - + +
313A SER* 3.9 2.5 - - - -
314A TYR* 2.9 32.6 + - - +
490A LEU* 3.7 25.8 - - + -
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Residues in contact with LEU 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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41A PHE* 4.9 2.0 - - + -
43A TYR* 3.9 11.2 - - + -
46A ASN* 3.7 33.7 - - + +
48A ILE* 3.8 35.4 - - + -
53A LEU* 5.6 3.6 - - + -
56A LEU* 5.0 7.4 - - + -
307A ILE* 3.0 38.7 + - + +
308A MSE 3.9 6.7 - - - +
310A LEU* 1.3 76.7 - - + +
312A ALA* 1.3 63.4 + - - +
314A TYR* 3.3 6.3 + - + +
315A TYR* 3.0 41.9 + - + +
461A THR* 4.4 5.4 - - - +
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Residues in contact with ALA 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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308A MSE 3.1 18.6 + - - +
309A ALA 3.8 1.1 - - - +
311A LEU* 1.3 77.7 - - - +
313A SER* 1.3 62.3 + - - +
315A TYR* 3.3 10.4 + - - +
316A SER* 3.0 24.0 + - - -
324A GLN* 3.3 30.6 - - - +
391A PRO* 5.5 1.9 - - - +
483A LYS* 3.6 10.3 - - - -
487A GLN* 3.4 17.5 - - - +
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Residues in contact with SER 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A PHE* 3.6 26.7 - - - -
309A ALA 2.9 14.6 + - - -
310A LEU* 4.9 0.4 - - - -
312A ALA* 1.3 73.6 - - - +
314A TYR* 1.3 65.9 + - - +
316A SER* 3.7 8.7 + - - -
317A CYS* 3.0 27.0 + - - +
487A GLN* 2.9 28.0 + - - +
490A LEU* 5.2 5.1 - - - +
491A TRP* 3.5 17.7 + - - -
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Residues in contact with TYR 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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3A PHE* 4.0 8.2 - - - -
8A LYS* 3.9 11.2 - - + -
11A LEU* 3.6 15.9 + - + +
12A LYS* 3.4 29.1 + - - +
47A LEU 4.0 18.0 + - - -
48A ILE* 4.9 4.3 - - + -
52A ILE* 4.0 17.2 - - + +
56A LEU* 4.0 32.5 - - + -
310A LEU 2.9 19.3 + - - +
311A LEU* 3.5 5.8 - - - +
313A SER* 1.3 75.6 - - - +
315A TYR* 1.3 72.1 + + - +
317A CYS* 3.6 1.9 - - - +
318A THR* 2.9 62.3 + - + -
319A TYR* 4.1 16.0 + + - -
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Residues in contact with TYR 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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46A ASN* 2.6 31.7 + - + +
47A LEU* 3.0 36.8 + - + -
311A LEU* 3.0 35.3 + - + +
312A ALA* 3.3 5.8 + - - +
314A TYR* 1.3 88.7 - + - +
316A SER* 1.3 57.3 + - - +
319A TYR* 2.9 43.2 + + - +
320A ASN 3.5 1.0 + - - -
321A SER* 3.3 11.0 + - - +
389A PHE* 3.7 25.4 - + + -
391A PRO* 3.5 40.6 - - + -
459A PRO* 3.3 10.4 - - + +
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Residues in contact with SER 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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312A ALA 3.0 17.0 + - - -
313A SER* 3.7 9.4 + - - -
315A TYR* 1.3 77.3 - - - +
317A CYS* 1.3 60.7 + - - +
320A ASN* 3.6 11.6 - - - +
321A SER* 3.5 24.7 - - - +
324A GLN* 6.5 0.2 - - - -
362A GLN* 3.4 28.6 + - - +
363A THR 4.7 0.5 + - - -
365A VAL* 3.8 16.8 - - - +
487A GLN* 5.1 0.3 + - - -
491A TRP* 3.9 16.5 - - - -
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Residues in contact with CYS 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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3A PHE* 4.6 4.5 - - + -
4A CYS* 2.1 57.9 - - + -
8A LYS* 3.9 10.5 - - + -
9A LYS* 3.6 18.1 + - - -
313A SER 3.0 18.5 + - - +
314A TYR* 3.6 4.3 - - - +
316A SER* 1.3 78.4 + - - +
318A THR* 1.3 70.1 + - + +
319A TYR 3.6 0.2 - - - -
320A ASN* 3.1 21.8 - - - +
362A GLN* 6.3 0.4 - - - -
491A TRP* 6.3 0.9 - - - +
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Residues in contact with THR 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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8A LYS* 3.3 50.0 - - + +
9A LYS* 4.0 12.9 + - - +
12A LYS* 3.5 24.5 - - - +
314A TYR* 2.9 43.4 + - + +
317A CYS* 1.3 76.9 - - - +
319A TYR* 1.3 79.4 + - - +
320A ASN* 3.4 6.7 + - - -
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Residues in contact with TYR 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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12A LYS* 3.5 40.8 + - + +
16A ILE* 5.9 1.0 + - - +
47A LEU* 3.7 27.7 + - + +
314A TYR* 4.1 13.6 + + - -
315A TYR* 2.9 35.3 + + - +
318A THR* 1.3 102.0 + - - +
320A ASN* 1.3 68.1 + - - +
321A SER* 3.1 4.0 + - - +
389A PHE* 3.5 51.7 - + + +
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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