Contacts of the helix formed by residues 286 - 298 (chain A) in PDB entry 4L1O
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 286 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A LEU* 4.6 10.8 - - - +
284A ILE* 3.4 1.7 - - - +
285A ILE* 1.3 85.3 - - - +
287A ALA* 1.3 65.3 + - - +
288A ARG* 3.8 7.8 + - - +
289A HIS* 3.3 30.1 + - - -
290A PHE* 2.9 19.4 + - - +
313A ARG* 3.4 14.0 - - - +
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Residues in contact with ALA 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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286A SER* 1.3 73.5 - - - +
288A ARG* 1.3 63.1 + - - +
290A PHE* 3.2 7.0 + - - +
291A GLN* 2.9 30.9 + - + +
313A ARG* 3.6 12.0 - - + +
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Residues in contact with ARG 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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286A SER* 3.2 8.9 + - - +
287A ALA* 1.3 79.3 - - - +
289A HIS* 1.3 71.0 + - + +
291A GLN* 3.4 5.3 + - - +
292A ARG* 3.0 28.3 + - + +
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Residues in contact with HIS 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A TRP* 4.2 18.6 + + - -
141A LEU* 4.3 13.9 - - + +
241A GLN* 5.5 0.9 - - - +
284A ILE* 3.7 17.9 - - + -
285A ILE* 3.7 17.9 - - + -
286A SER* 3.3 20.3 + - - +
288A ARG* 1.3 90.5 - - + +
290A PHE* 1.3 66.4 + - - +
292A ARG* 3.2 35.4 + - - +
293A VAL* 2.9 30.2 + - + +
335A PHE 6.1 0.4 - - - +
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Residues in contact with PHE 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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284A ILE* 3.4 13.6 - - + +
286A SER 2.9 15.0 + - - +
287A ALA* 3.2 11.4 + - - +
289A HIS* 1.3 75.6 - - - +
291A GLN* 1.3 86.3 + - + +
293A VAL* 3.4 0.5 + - - -
294A MET* 3.0 51.6 + - + +
308A GLY 4.3 2.0 - - - -
309A ASP 3.7 11.0 - - - -
310A ALA* 3.5 30.5 - - + -
313A ARG* 3.7 26.7 - - + -
314A TYR 3.3 23.6 - - - -
315A ILE* 3.7 20.6 - - + +
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Residues in contact with GLN 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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287A ALA* 2.9 22.2 + - + +
288A ARG* 3.8 5.8 - - - +
290A PHE* 1.3 102.4 - - - +
292A ARG* 1.3 57.9 + - - +
294A MET* 3.9 5.6 - - - +
295A GLY* 2.9 26.9 + - - -
310A ALA* 4.5 9.3 - - - +
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Residues in contact with ARG 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A TRP* 6.3 0.2 - - - -
288A ARG* 3.0 19.2 + - + +
289A HIS* 3.2 36.0 + - - +
290A PHE 3.3 0.2 - - - -
291A GLN* 1.3 77.9 - - - +
293A VAL* 1.3 73.9 + - - +
295A GLY* 3.4 2.3 + - - -
296A LEU* 3.3 29.5 + - + +
332A GLU* 2.8 42.6 + - - +
333A GLU 3.2 10.8 + - - -
334A ILE 3.0 29.3 + - - -
335A PHE* 3.7 17.4 + - - +
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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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284A ILE* 4.9 4.5 - - + -
289A HIS* 2.9 22.3 + - + +
292A ARG* 1.3 98.3 - - - +
294A MET* 1.3 66.7 + - - +
296A LEU* 3.1 22.1 + - + +
297A ILE* 3.5 8.1 + - - +
315A ILE* 3.5 25.1 - - + -
334A ILE* 3.8 14.1 - - + +
335A PHE 4.1 9.0 - - - +
336A GLY* 4.3 13.5 - - - -
337A PRO* 4.4 0.7 - - + -
338A VAL* 3.8 23.8 - - + -
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Residues in contact with MET 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 PHE* 3.0 44.4 + - + +
291A GLN* 3.9 8.7 - - - +
293A VAL* 1.3 76.9 - - - +
295A GLY* 1.3 63.5 + - - +
297A ILE* 3.1 34.2 + - + +
298A GLU* 3.6 10.2 + - - +
306A GLY 4.2 9.6 - - - +
307A THR* 4.1 4.9 - - - +
308A GLY* 3.8 28.0 - - - +
315A ILE* 3.8 26.5 - - + -
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Residues in contact with GLY 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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291A GLN 2.9 17.8 + - - -
292A ARG* 3.7 3.8 - - - -
293A VAL 3.2 0.2 - - - -
294A MET* 1.3 77.0 - - - +
296A LEU* 1.3 60.1 + - - +
298A GLU* 3.1 37.4 + - - +
328A PRO* 5.8 1.7 - - - +
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Residues in contact with LEU 296 (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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292A ARG* 3.3 36.7 + - - +
293A VAL* 3.1 14.5 + - + +
295A GLY* 1.3 75.4 - - - +
297A ILE* 1.3 60.9 + - + +
298A GLU 3.6 2.2 + - - +
300A GLN* 3.3 18.5 + - - +
320A LEU* 5.3 0.2 - - - -
328A PRO* 3.7 35.1 - - + +
329A VAL* 3.7 22.7 + - + +
332A GLU* 3.6 29.6 - - + +
334A ILE* 4.2 28.3 - - + -
338A VAL* 5.5 2.0 - - + -
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Residues in contact with ILE 297 (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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293A VAL 3.7 10.5 - - - +
294A MET* 3.1 38.2 + - + +
296A LEU* 1.3 76.6 - - - +
298A GLU* 1.3 63.9 + - - +
299A GLY 3.4 0.2 + - - -
300A GLN* 3.0 24.0 + - - +
302A VAL* 3.9 25.8 - - + -
306A GLY* 4.4 16.4 - - - +
315A ILE* 4.3 8.5 - - + -
318A THR* 4.4 8.7 - - + +
320A LEU* 4.4 9.2 - - + -
338A VAL* 3.8 31.9 - - + -
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Residues in contact with GLU 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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294A MET 3.8 9.1 - - - +
295A GLY* 3.1 28.8 + - - +
296A LEU 4.0 1.7 - - - +
297A ILE* 1.3 78.7 - - + +
299A GLY* 1.3 61.9 + - - +
300A GLN* 3.4 7.4 + - - +
328A PRO* 5.7 4.3 - - - +
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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