Contacts of the helix formed by residues 289 - 306 (chain A) in PDB entry 4LZ6
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 MET 289 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A MET* 2.6 46.0 + - + +
286A MET* 2.9 15.6 + - + +
288A VAL* 1.3 118.7 - - + +
290A MET* 1.3 53.0 + - - +
291A PRO* 3.5 0.8 - - - +
292A MET* 2.5 43.3 + - + +
293A MET* 3.0 23.0 + - + +
333A ILE* 4.0 19.5 - - + +
337A LEU* 6.0 0.7 - - + -
369A THR* 5.6 3.6 - - + -
372A ILE* 5.5 12.3 - - + -
376A ILE* 5.8 6.3 - - - -
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Residues in contact with MET 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A MET* 3.1 22.9 - - + +
30A MET* 3.3 26.0 - - + +
31A PHE* 2.6 52.0 - - + -
34A ALA* 4.6 3.1 - - + -
286A MET* 2.9 10.3 + - + +
287A PHE* 3.2 37.6 + - + +
289A MET* 1.3 69.9 - - - +
291A PRO* 1.4 77.4 - - + -
292A MET 2.7 1.7 + - - -
293A MET* 2.7 13.7 + - - +
294A GLY* 2.6 24.2 + - - -
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Residues in contact with PRO 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A MET* 2.9 33.2 - - + +
287A PHE* 3.6 13.0 - - + +
288A VAL* 4.2 13.5 - - + -
289A MET 3.8 4.7 - - - +
290A MET* 1.4 95.4 - - + +
292A MET* 1.3 61.7 + - - +
295A ILE* 3.1 12.4 - - - +
329A PHE* 4.4 15.8 - - + -
333A ILE* 3.9 18.2 - - + -
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Residues in contact with MET 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A MET* 2.5 23.2 + - + +
290A MET 2.9 1.1 - - - -
291A PRO* 1.3 70.2 - - - +
293A MET* 1.3 70.0 + - + +
294A GLY 2.6 2.8 + - - -
295A ILE* 2.8 15.8 + - + +
296A MET* 2.9 12.1 + - - +
326A ALA* 3.3 24.7 - - + +
329A PHE* 3.2 42.4 - - - +
330A SER* 3.0 30.1 - - - +
333A ILE* 4.1 8.1 - - + -
369A THR* 5.0 2.5 - - + +
372A ILE* 4.7 7.9 - - + -
373A GLY* 3.5 11.0 - - - +
376A ILE* 4.6 24.7 - - + -
377A VAL* 6.0 0.2 - - + -
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Residues in contact with MET 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A MET* 2.9 36.1 - - + -
286A MET* 5.2 2.2 - - + +
289A MET* 3.0 16.5 + - + -
290A MET* 2.7 14.9 + - - +
292A MET* 1.3 75.5 - - + +
294A GLY* 1.3 55.2 + - - +
296A MET* 2.9 38.1 - - + +
297A GLN* 3.0 18.6 + - - +
376A ILE* 3.2 37.5 - - + -
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Residues in contact with GLY 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A SER* 3.7 12.6 - - - -
26A ALA* 3.9 5.5 - - - +
27A MET* 3.3 26.2 - - - -
30A MET* 4.4 1.8 - - - -
290A MET 2.6 15.1 + - - -
292A MET 2.6 1.4 + - - -
293A MET* 1.3 71.3 - - - +
295A ILE* 1.3 63.6 + - - +
297A GLN* 3.2 16.4 + - - +
298A ALA 3.3 13.9 + - - -
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Residues in contact with ILE 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 5.5 2.7 - - + -
20A ARG* 4.8 11.4 - - - +
23A SER* 3.7 18.8 - - - +
27A MET* 3.3 16.5 - - + +
291A PRO 3.1 18.4 - - - +
292A MET* 2.8 8.9 + - + +
294A GLY* 1.3 73.7 - - - +
296A MET* 1.3 67.7 + - - +
298A ALA* 3.2 16.7 + - + +
299A MET* 3.6 19.1 - - + +
322A GLY 4.4 3.4 - - - +
325A VAL* 3.8 46.2 - - + -
326A ALA* 4.6 6.5 - - + +
329A PHE* 4.2 10.5 - - + -
377A VAL* 6.4 0.4 - - + -
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Residues in contact with MET 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ILE* 5.6 7.2 - - + -
292A MET 2.9 8.7 + - - +
293A MET* 2.9 34.3 - - + +
295A ILE* 1.3 75.2 - - - +
297A GLN* 1.3 66.5 + - + +
298A ALA 2.7 13.3 + - - -
299A MET* 2.8 25.7 + - - +
300A GLN* 3.3 39.3 + - + +
376A ILE* 4.6 19.3 - - + +
377A VAL* 5.7 5.2 - - - +
380A GLY* 5.0 17.9 - - - -
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Residues in contact with GLN 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 4.7 4.7 - - - +
26A ALA* 3.0 26.3 - - + +
30A MET* 3.9 17.3 - - - +
161A ARG* 2.6 38.1 - - - +
293A MET* 3.0 15.6 + - - +
294A GLY* 3.2 16.3 + - - +
296A MET* 1.3 85.3 - - + +
298A ALA* 1.3 61.0 + - - +
300A GLN* 3.4 44.0 - - - +
301A PRO* 3.8 3.8 - - - +
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Residues in contact with ALA 298 (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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19A LEU* 3.4 22.0 - - + +
22A LEU* 3.2 23.6 - - + +
23A SER* 3.6 33.2 - - - +
294A GLY 3.3 3.0 + - - -
295A ILE* 3.2 14.5 + - + +
296A MET 2.7 5.5 + - - -
297A GLN* 1.3 75.8 - - - +
299A MET* 1.3 53.2 + - - +
301A PRO* 2.7 23.6 - - - +
302A ILE* 3.6 4.3 + - - +
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Residues in contact with MET 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 3.8 19.5 - - + -
295A ILE* 3.6 20.2 - - + +
296A MET* 2.8 16.8 + - - +
298A ALA* 1.3 69.2 - - - +
300A GLN* 1.3 67.8 + - - +
301A PRO* 2.9 4.9 - - - -
302A ILE* 3.7 7.6 - - - -
303A VAL* 3.2 38.1 + - + +
318A THR* 4.1 12.3 - - + -
319A VAL* 5.2 2.7 - - - -
322A GLY* 2.7 43.3 - - - +
377A VAL* 4.4 11.7 - - + -
380A GLY 6.5 0.7 - - - -
381A LEU* 4.0 22.7 - - + -
384A SER* 4.0 3.0 - - - -
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Residues in contact with GLN 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ILE* 5.3 4.8 - - + +
78A ALA* 4.0 15.5 - - + +
79A SER* 5.5 1.6 - - - -
82A SER* 4.5 5.4 + - - -
158A ASN* 3.4 28.0 + - - +
161A ARG* 3.4 33.2 - - - +
162A SER* 4.1 2.8 + - - -
296A MET* 3.3 32.6 + - + +
297A GLN* 3.4 36.5 - - - +
299A MET* 1.3 75.0 - - - +
301A PRO* 1.3 67.3 - - + +
304A GLY 4.5 0.2 + - - -
380A GLY* 5.8 2.9 - - - -
384A SER* 3.1 27.0 - - - -
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Residues in contact with PRO 301 (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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22A LEU* 4.1 13.2 - - + -
82A SER* 4.4 5.0 - - - -
161A ARG* 3.2 29.2 - - + +
162A SER* 3.6 21.3 - - - +
163A GLU 4.0 7.0 - - - +
297A GLN 3.8 2.2 - - - +
298A ALA 2.7 30.3 - - - +
300A GLN* 1.3 91.1 - - + +
302A ILE* 1.3 63.1 + - - +
304A GLY* 2.9 23.0 + - - +
305A TYR* 3.1 15.0 + - + -
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Residues in contact with ILE 302 (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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15A ILE* 4.6 6.5 - - + -
18A LEU* 3.3 59.5 - - + +
19A LEU* 3.4 18.8 - - + +
22A LEU* 4.2 8.3 - - + -
298A ALA 3.8 12.1 - - - +
299A MET* 3.3 2.9 + - - -
301A PRO* 1.3 80.0 - - - +
303A VAL* 1.3 57.1 + - + +
304A GLY 2.4 15.4 + - - -
305A TYR* 3.3 17.6 + - + -
306A ASN* 3.6 17.1 + - + +
315A LEU* 6.3 0.2 - - + -
318A THR* 3.3 35.9 - - + +
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Residues in contact with VAL 303 (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 MET* 3.2 33.6 + - + +
302A ILE* 1.3 76.7 - - - +
304A GLY* 1.3 56.0 + - - +
307A TYR* 4.0 9.0 - - - +
315A LEU* 4.0 21.8 - - + +
318A THR* 3.9 22.0 - - + -
319A VAL* 4.0 11.0 - - + -
381A LEU* 4.0 19.1 - - + -
384A SER* 3.5 13.7 - - - +
385A LEU* 3.0 39.9 - - + +
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Residues in contact with GLY 304 (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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82A SER* 2.8 42.3 - - - +
83A ARG* 3.7 1.4 + - - -
300A GLN 4.5 1.3 - - - -
301A PRO* 2.9 13.4 + - - -
302A ILE 2.4 15.8 + - - -
303A VAL* 1.3 72.4 - - - +
305A TYR* 1.3 49.7 + - - -
306A ASN 3.2 0.9 - - - -
307A TYR 2.1 27.2 - - - +
384A SER 4.8 3.1 - - - -
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Residues in contact with TYR 305 (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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10A LEU* 4.0 3.1 - - + +
11A GLY* 3.0 43.4 + - - -
12A THR 2.7 22.7 + - - -
13A GLU* 3.8 6.5 - - - -
18A LEU* 3.0 20.1 - - + +
82A SER* 3.8 8.0 + - - +
85A LEU* 4.2 11.2 - - + +
86A GLY* 3.3 27.8 - - - +
163A GLU 5.4 8.3 - - - -
301A PRO* 3.1 17.6 + - + -
302A ILE* 3.3 9.9 + - + -
304A GLY* 1.3 70.5 - - - +
306A ASN* 1.3 83.5 + - - +
307A TYR 3.3 6.4 - - - +
310A LYS* 3.3 22.7 - - + +
311A GLN* 6.2 0.2 - - - -
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Residues in contact with ASN 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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13A GLU* 2.7 42.6 + - - +
18A LEU* 5.6 0.2 - - - +
302A ILE* 3.6 12.8 + - + +
304A GLY 3.2 0.8 - - - -
305A TYR* 1.3 102.7 - - - +
307A TYR* 1.3 61.6 + - - +
310A LYS* 3.3 27.8 + - - +
311A GLN* 3.0 42.3 + - - +
312A TYR* 3.9 7.3 - - - -
314A ARG* 4.1 1.7 - - - +
315A LEU* 4.2 16.6 - - + -
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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