Contacts of the helix formed by residues 284 - 295 (chain A) in PDB entry 5L0P
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 THR 284 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282A LYS* 3.4 10.2 + - + +
283A VAL* 1.3 80.4 - - - +
285A LEU* 1.3 63.7 + - - +
286A PRO* 3.5 13.2 - - - +
287A ARG* 3.0 36.0 + - - +
288A LEU* 2.9 31.0 + - - +
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Residues in contact with LEU 285 (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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283A VAL* 5.7 1.6 - - + -
284A THR* 1.3 71.8 - - - +
286A PRO* 1.4 72.6 - - + +
288A LEU* 3.3 19.6 + - + +
289A LYS* 3.1 53.3 + - - +
318A ILE* 5.9 0.9 - - + -
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Residues in contact with PRO 286 (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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284A THR* 3.5 15.9 - - + +
285A LEU* 1.4 92.7 - - + +
287A ARG* 1.3 57.5 + - - +
289A LYS* 4.0 1.2 - - - +
290A ILE* 3.1 33.4 + - - +
318A ILE* 3.8 27.8 - - + +
322A THR* 4.1 25.4 - - + -
325A ARG* 5.9 0.2 - - - +
326A VAL* 4.7 5.6 - - + -
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Residues in contact with ARG 287 (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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276A LEU* 3.7 17.3 - - + -
281A LEU* 3.7 22.3 - - - +
282A LYS* 2.7 59.0 + - - +
284A THR* 3.0 26.6 + - - +
286A PRO* 1.3 72.3 - - - +
288A LEU* 1.3 60.5 + - - +
290A ILE 3.6 0.3 + - - -
291A LEU* 2.8 34.2 + - - +
326A VAL* 3.9 12.5 - - + +
329A GLN* 3.4 36.6 + - - +
330A PHE* 3.5 30.4 - - + -
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Residues in contact with LEU 288 (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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272A ASN* 3.7 29.2 + - + +
273A ASN* 3.2 34.5 - - - +
276A LEU* 3.8 16.4 - - + -
283A VAL* 3.7 11.9 - - + -
284A THR 2.9 20.3 + - - +
285A LEU* 3.8 22.0 - - + +
287A ARG* 1.3 72.7 - - - +
289A LYS* 1.3 55.3 + - + +
291A LEU* 3.4 4.2 + - + +
292A GLU* 2.7 35.5 + - - +
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Residues in contact with LYS 289 (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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285A LEU* 3.1 42.3 + - - +
286A PRO 4.0 2.2 - - - +
288A LEU* 1.3 77.5 - - + +
290A ILE* 1.3 53.7 + - - +
292A GLU* 3.0 10.1 + - - +
293A VAL* 2.7 37.1 + - - +
311A LEU* 3.8 17.3 - - + -
316A GLU* 2.3 44.8 + - + +
317A GLU 5.4 1.6 - - - +
318A ILE* 3.6 18.2 - - + +
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Residues in contact with ILE 290 (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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286A PRO* 3.1 20.1 + - + +
287A ARG 4.0 2.5 - - - +
289A LYS* 1.3 71.0 - - - +
291A LEU* 1.3 67.2 + - - +
293A VAL* 3.3 2.9 + - - +
294A LEU* 3.0 25.0 + - + +
307A LEU* 3.4 31.4 - - + -
311A LEU* 3.8 19.7 - - + -
318A ILE* 4.8 5.8 - - + -
323A VAL* 3.9 28.5 - - + +
326A VAL* 3.7 35.7 - - + -
327A LEU* 3.9 17.3 - - + -
330A PHE* 4.2 4.5 - - + -
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Residues in contact with LEU 291 (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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272A ASN* 3.8 31.4 - - + +
275A ALA* 4.4 9.6 - - + -
276A LEU* 3.9 31.0 - - + -
287A ARG 2.8 20.1 + - - +
288A LEU* 3.5 5.2 - - - +
290A ILE* 1.3 78.1 - - - +
292A GLU* 1.3 61.5 + - - +
294A LEU* 3.2 4.8 + - + +
295A GLN* 3.1 31.0 + - - +
330A PHE* 3.9 9.6 - - + -
335A ILE* 4.2 17.0 - - + -
350A LEU* 3.8 26.5 - - + -
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Residues in contact with GLU 292 (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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272A ASN* 4.2 6.7 - - - +
288A LEU 2.7 17.7 + - - +
289A LYS* 3.1 15.3 - - + +
291A LEU* 1.3 73.3 - - - +
293A VAL* 1.3 61.0 + - + +
295A GLN* 3.1 23.0 + - - +
296A GLU* 3.4 13.8 + - - +
314A MET* 6.2 4.0 - - + -
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Residues in contact with VAL 293 (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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289A LYS 2.7 11.9 + - - +
290A ILE 3.3 6.7 + - - +
292A GLU* 1.3 71.8 - - - +
294A LEU* 1.3 60.0 + - - +
296A GLU* 3.2 19.2 + - - +
299A ASN* 3.1 26.8 - - + +
302A VAL* 5.1 1.1 - - + -
307A LEU* 3.5 31.0 - - + -
310A ARG* 3.9 31.2 - - + -
311A LEU* 3.7 30.1 - - + -
314A MET* 4.0 16.6 - - - -
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Residues in contact with LEU 294 (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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290A ILE 3.0 19.7 + - - +
291A LEU* 3.5 9.4 - - - +
293A VAL* 1.3 76.2 - - - +
295A GLN* 1.3 58.9 + - - +
296A GLU 3.6 0.2 + - - -
299A ASN 3.6 4.9 - - - +
300A HIS* 3.0 52.4 + - - +
302A VAL* 3.7 19.5 - - + -
307A LEU* 4.2 8.5 - - + -
327A LEU* 4.0 17.3 - - + -
330A PHE* 4.2 12.1 - - + -
336A VAL* 3.7 25.6 - - + -
348A PHE 4.0 7.6 - - - +
350A LEU* 3.7 25.6 - - + +
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Residues in contact with GLN 295 (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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272A ASN* 2.9 42.0 + - - +
275A ALA* 5.6 2.2 - - - +
291A LEU* 3.1 27.0 + - + +
292A GLU* 3.1 10.6 + - - +
294A LEU* 1.3 75.0 - - - +
296A GLU* 1.3 63.2 + - - +
297A PRO* 3.7 3.6 - - - +
300A HIS* 3.7 12.5 - - - -
350A LEU* 3.9 18.3 - - + +
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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