Contacts of the helix formed by residues 318 - 338 (chain A) in PDB entry 1L4E
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 GLY 318 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A VAL* 4.4 8.2 - - - +
99A VAL* 3.1 7.4 - - - +
172A VAL 3.5 22.2 - - - -
173A GLY* 3.7 3.7 - - - -
263A ASP* 2.9 17.3 + - - -
317A GLU* 1.3 76.8 - - - +
319A SER* 1.3 65.1 + - - +
320A GLY 3.2 2.7 - - - -
321A ALA* 3.3 5.7 + - - +
322A ALA* 3.1 21.8 + - - +
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Residues in contact with SER 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A VAL* 2.8 17.8 - - - +
102A LEU* 3.4 31.9 - - - +
263A ASP* 3.7 0.7 + - - -
289A HIS* 5.7 0.3 - - - -
313A MET* 4.0 12.0 - - - +
315A LEU* 3.9 20.8 + - - +
316A GLY 2.7 27.9 + - - -
318A GLY* 1.3 78.8 - - - +
320A GLY* 1.3 62.2 + - - +
322A ALA* 3.5 2.5 + - - +
323A LEU* 3.2 18.0 + - - +
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Residues in contact with GLY 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ASP* 2.7 20.9 + - - -
288A SER* 3.4 14.5 - - - -
289A HIS* 3.5 20.8 - - - -
309A LEU* 4.6 1.7 - - - +
313A MET* 4.0 10.7 - - - +
319A SER* 1.3 73.2 + - - +
321A ALA* 1.3 64.0 + - - +
323A LEU* 3.2 6.5 + - - +
324A ALA* 3.1 17.3 + - - +
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Residues in contact with ALA 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A VAL* 5.2 1.3 - - + -
171A GLY* 4.0 17.7 - - - -
172A VAL 4.2 10.5 - - - +
261A LEU* 3.6 22.7 - - + +
262A LEU 3.6 21.5 + - - +
263A ASP* 3.5 4.2 + - + -
288A SER* 3.8 4.9 + - - -
318A GLY* 3.3 9.8 + - - +
320A GLY* 1.3 76.1 - - - +
322A ALA* 1.3 62.3 + - - +
324A ALA* 3.2 9.5 + - - -
325A MET* 3.3 17.8 + - - +
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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
----------------------------------------------------------
63A VAL* 4.5 7.8 - - + +
99A VAL* 4.5 3.4 - - + +
102A LEU* 3.9 10.0 - - + +
103A ALA* 3.8 35.2 - - + +
106A ALA* 3.6 8.4 - - - +
318A GLY 3.1 15.0 + - - +
319A SER* 3.8 5.8 - - - +
321A ALA* 1.3 76.2 - - - +
323A LEU* 1.3 61.9 + - - +
325A MET* 3.3 24.1 + - - +
326A PRO* 3.6 8.3 - - - +
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Residues in contact with LEU 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 4.5 23.7 - - + +
289A HIS* 5.9 0.4 - - + -
309A LEU* 3.8 24.2 - - + +
311A MET* 4.0 17.5 - - + -
313A MET* 3.8 30.7 - - + -
319A SER 3.2 13.6 + - - +
320A GLY* 3.2 10.0 + - - +
322A ALA* 1.3 77.9 - - - +
324A ALA* 1.3 58.4 + - - +
326A PRO* 3.2 16.9 - - - +
327A ILE* 5.0 2.6 - - - +
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Residues in contact with ALA 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU* 4.4 11.9 - - + -
287A PRO 4.9 0.9 - - - +
288A SER* 3.7 35.2 - - - +
308A TYR* 5.4 2.7 - - + -
309A LEU* 4.0 12.6 - - + -
320A GLY 3.1 5.1 + - - +
321A ALA 3.2 3.6 + - - +
322A ALA 3.2 0.4 - - - -
323A LEU* 1.3 75.4 - - - +
325A MET* 1.3 65.7 + - - +
326A PRO* 3.2 3.4 - - - -
327A ILE* 2.9 30.1 + - + +
328A VAL* 3.4 6.5 + - + +
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Residues in contact with MET 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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61A LYS* 3.9 25.4 - - + -
62A ALA 3.9 13.7 - - - +
63A VAL* 3.9 22.4 - - + -
106A ALA* 4.0 8.5 - - + +
108A ALA* 3.7 25.4 - - - -
169A LEU* 4.3 12.2 - - + +
170A PHE 4.2 5.8 - - - -
171A GLY* 4.1 13.2 - - - +
261A LEU* 3.6 16.8 - - + -
321A ALA 3.3 13.8 + - - +
322A ALA* 3.3 14.5 + - - +
324A ALA* 1.3 76.9 - - - +
326A PRO* 1.3 69.8 - - + +
328A VAL* 3.1 16.5 + - - +
329A GLU* 3.1 16.7 + - - +
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Residues in contact with PRO 326 (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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105A GLN 5.8 0.7 - - - +
106A ALA* 4.2 15.7 - - + -
322A ALA 3.6 6.1 - - - +
323A LEU* 3.2 18.6 - - - +
324A ALA 3.3 0.2 - - - -
325A MET* 1.3 96.1 - - + +
327A ILE* 1.3 58.0 + - + +
329A GLU* 3.4 14.8 + - - +
330A ALA* 2.9 28.6 + - - +
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Residues in contact with ILE 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 3.8 20.2 - - + +
42A LEU* 4.2 11.2 - - + -
308A TYR* 4.1 30.5 - - + -
309A LEU* 4.0 32.1 - - + -
323A LEU 5.0 2.7 - - - +
324A ALA* 2.9 23.3 + - + +
326A PRO* 1.3 76.9 - - + +
328A VAL* 1.3 67.7 + - + +
330A ALA* 3.1 16.0 + - - +
331A ALA* 3.1 10.9 + - - +
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Residues in contact with VAL 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 4.0 17.5 - - + -
46A LEU* 3.9 25.8 - - + -
58A VAL* 3.7 22.4 - - + -
169A LEU* 4.0 15.3 - - + -
259A PRO* 6.1 0.2 - - + -
261A LEU* 4.2 29.6 - - + -
286A ILE* 4.7 10.3 - - + -
308A TYR* 6.2 0.7 - - + -
324A ALA 4.0 10.8 - - - +
325A MET 3.1 6.9 + - - +
327A ILE* 1.3 76.4 - - + +
329A GLU* 1.3 63.0 + - - +
331A ALA* 3.3 12.0 + - - +
332A CYS* 3.3 13.7 + - - -
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Residues in contact with GLU 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A VAL* 4.0 25.1 - - + +
61A LYS* 2.8 38.7 + - + +
106A ALA* 4.7 3.3 - - - +
325A MET* 3.1 12.6 + - - +
326A PRO* 3.7 18.3 - - - +
328A VAL* 1.3 76.8 - - - +
330A ALA* 1.3 57.5 + - - +
332A CYS* 3.2 8.1 + - - +
333A ALA* 3.0 29.0 + - - +
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Residues in contact with ALA 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 4.3 15.3 - - + +
326A PRO 2.9 14.5 + - - +
327A ILE* 3.1 13.9 + - - +
329A GLU* 1.3 78.1 - - - +
331A ALA* 1.3 57.5 + - - +
333A ALA* 3.3 6.8 + - - +
334A MET* 2.9 29.5 + - - +
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Residues in contact with ALA 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 3.6 40.8 - - + +
42A LEU* 3.9 20.6 - - + -
43A ALA* 4.0 10.5 - - + +
46A LEU* 4.7 2.9 - - + -
327A ILE 3.1 5.3 + - - -
328A VAL 3.3 8.5 + - - +
330A ALA* 1.3 76.7 - - - +
332A CYS* 1.3 61.6 + - - +
334A MET* 3.6 8.7 - - - +
335A PHE* 3.2 22.5 + - - +
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Residues in contact with CYS 332 (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 LEU* 4.1 8.7 - - - -
56A PRO* 3.5 22.0 - - - +
57A GLN* 3.4 40.2 - - - -
58A VAL* 3.9 11.2 - - + +
328A VAL 3.3 13.7 + - - -
329A GLU* 3.2 9.3 + - - +
330A ALA 3.2 0.6 - - - -
331A ALA* 1.3 78.2 - - - +
333A ALA* 1.3 60.2 + - - +
335A PHE* 3.3 1.2 + - - +
336A HIS* 3.0 38.2 + - + -
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Residues in contact with ALA 333 (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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329A GLU 3.0 16.8 + - - +
330A ALA* 3.7 8.1 - - - +
332A CYS* 1.3 73.6 - - - +
334A MET* 1.3 57.5 + - - +
336A HIS* 5.0 1.1 - - - -
337A ASN* 2.7 53.6 + - + +
338A MET 4.0 0.2 + - - -
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Residues in contact with MET 334 (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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26A ILE* 4.1 20.9 - - + -
29A LEU* 4.0 8.2 - - + +
31A LYS* 4.9 0.9 - - - -
36A LEU* 3.5 28.9 - - + -
39A LEU* 3.9 21.8 - - + +
40A GLU* 4.2 9.2 - - + -
43A ALA* 3.8 22.0 - - + -
330A ALA 2.9 17.3 + - - +
331A ALA* 3.6 16.2 - - - +
333A ALA* 1.3 78.7 - - - +
335A PHE* 1.3 67.2 + - - +
338A MET* 3.1 61.0 + - + +
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Residues in contact with PHE 335 (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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21A ARG 5.2 0.2 - - - -
22A THR* 3.2 49.4 - - + -
25A HIS* 3.1 55.6 - + + -
26A ILE* 3.6 19.3 - - + -
29A LEU* 4.4 6.7 - - - +
43A ALA* 4.6 0.4 - - + -
54A GLY 5.9 0.7 - - - -
55A THR* 3.8 9.4 - - - -
56A PRO* 3.7 28.7 - - + -
331A ALA 3.2 11.7 + - - +
332A CYS 3.5 8.3 - - - +
333A ALA 3.3 0.2 - - - -
334A MET* 1.3 88.8 - - + +
336A HIS* 1.3 82.3 + + + +
338A MET 4.7 0.5 + - - +
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Residues in contact with HIS 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A HIS* 5.3 2.4 - - - -
55A THR* 3.0 27.2 + - + +
56A PRO 2.7 27.6 + - - -
57A GLN* 4.8 3.7 - - + +
332A CYS* 3.0 30.3 + - + +
333A ALA* 5.0 0.4 - - - -
335A PHE* 1.3 91.7 - + - +
337A ASN* 1.3 74.6 + - - +
338A MET 3.8 2.3 - - - +
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Residues in contact with ASN 337 (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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333A ALA* 2.7 36.1 + - + +
336A HIS* 1.3 89.9 + - - +
338A MET* 1.3 65.4 + - - +
339A GLY 3.7 0.3 + - - -
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Residues in contact with MET 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A HIS* 5.6 1.6 - - - -
29A LEU* 4.3 27.2 - - + +
30A LEU* 5.1 9.2 - - + +
31A LYS* 4.6 7.4 - - - -
36A LEU* 3.2 34.5 - - + -
39A LEU* 6.1 0.2 - - + -
334A MET* 3.1 43.5 + - + +
335A PHE 5.2 0.9 - - - +
336A HIS 3.8 2.8 - - - +
337A ASN* 1.3 80.1 + - - +
339A GLY* 1.3 69.7 + - - +
340A GLU* 4.7 2.8 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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