Contacts of the helix formed by residues 284 - 300 (chain A) in PDB entry 3N00
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).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A PRO* 1.3 79.8 - - + +
285A VAL* 1.3 64.4 + - - +
286A GLU* 3.1 9.2 + - - +
287A ASP* 2.5 41.5 + - - +
288A VAL* 3.2 12.4 + - - +
568A ARG* 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A PRO 3.7 1.4 + - - -
284A THR* 1.3 71.9 - - - +
286A GLU* 1.3 58.0 + - - +
288A VAL* 3.6 7.0 + - - +
289A ILE* 3.1 37.5 + - + +
568A ARG* 3.9 36.3 - - + +
569A ALA* 3.9 15.7 - - - -
572A ALA* 3.7 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A THR* 3.1 8.1 + - - +
285A VAL* 1.3 77.0 - - - +
287A ASP* 1.3 59.8 + - - +
289A ILE* 3.5 8.5 + - - +
290A SER* 2.9 32.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A PRO* 4.2 13.3 - - + +
284A THR* 2.5 46.0 + - - +
286A GLU* 1.3 76.5 - - - +
288A VAL* 1.3 52.0 - - - +
290A SER* 3.3 5.0 + - - -
291A GLN* 2.7 44.2 + - - +
458A PRO* 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A PRO* 3.6 34.8 - - + +
284A THR 3.2 7.9 + - - +
285A VAL* 3.8 7.6 - - - +
287A ASP* 1.3 75.5 - - - +
289A ILE* 1.3 66.9 + - - +
291A GLN* 3.8 0.2 - - - +
292A VAL* 2.9 28.8 + - + +
458A PRO* 4.2 15.5 - - + -
539A LEU* 4.1 5.2 - - + -
565A THR* 4.2 15.3 - - + -
566A LEU* 3.9 26.2 - - + -
568A ARG* 5.3 0.7 - - - +
569A ALA* 3.8 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A VAL* 3.1 33.0 + - + +
286A GLU* 3.8 7.6 - - - +
288A VAL* 1.3 77.5 - - - +
290A SER* 1.3 58.4 + - - +
292A VAL* 4.1 1.1 - - - +
293A ALA* 3.0 34.1 + - - +
535A GLU* 3.8 25.1 - - + +
539A LEU* 3.9 25.1 - - + +
569A ALA* 4.2 6.3 - - + +
572A ALA* 5.1 0.4 - - + -
573A LEU* 3.9 44.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A GLU 2.9 19.5 + - - -
287A ASP* 3.5 6.1 - - - -
289A ILE* 1.3 79.1 - - - +
291A GLN* 1.3 64.1 + - - +
293A ALA* 3.8 3.6 - - - +
294A ARG* 3.1 30.9 + - - +
297A ARG* 5.6 0.2 + - - -
535A GLU* 5.5 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ASP* 2.7 26.1 + - - +
288A VAL 3.8 2.0 - - - +
290A SER* 1.3 75.9 + - - +
292A VAL* 1.3 62.1 + - - +
294A ARG* 3.5 7.7 + - - +
295A ALA* 3.1 22.9 + - - +
456A HIS* 3.2 29.8 + - + +
458A PRO* 3.9 27.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A VAL* 2.9 23.0 + - + +
289A ILE 4.2 1.1 - - - +
291A GLN* 1.3 73.2 - - - +
293A ALA* 1.3 58.9 + - - +
295A ALA* 3.3 7.0 + - - +
296A HIS* 2.9 27.2 + - - +
453A PHE* 3.8 12.6 - - + -
456A HIS 5.2 1.6 - - - -
457A ILE* 4.7 6.1 - - + +
458A PRO* 3.8 22.2 - - + -
538A GLY 3.3 34.3 - - - +
539A LEU* 3.7 25.4 - - + -
542A ALA* 4.2 5.6 - - + -
566A LEU* 4.3 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ILE* 3.0 21.4 + - + +
290A SER* 3.8 4.0 - - - +
292A VAL* 1.3 78.3 - - - +
294A ARG* 1.3 57.4 + - - +
296A HIS* 3.5 8.6 + - - +
297A ARG* 3.0 45.2 + - - +
534A GLU* 5.2 1.6 - - - +
535A GLU* 3.7 38.6 - - + +
538A GLY* 5.2 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A SER* 3.1 21.3 + - - +
291A GLN* 3.6 7.4 - - - +
293A ALA* 1.3 75.7 - - - +
295A ALA* 1.3 60.9 + - - +
297A ARG* 3.0 19.7 + - - +
298A GLU* 2.8 56.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A GLN 3.1 10.6 + - - +
292A VAL* 3.6 9.0 - - - +
294A ARG* 1.3 78.9 - - - +
296A HIS* 1.3 57.0 + - - +
298A GLU* 3.9 10.0 - - - -
299A ILE* 2.9 38.7 + - + +
453A PHE* 4.0 14.1 - - + -
456A HIS* 3.4 39.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A VAL 2.9 16.7 + - - +
293A ALA 3.6 5.3 + - - +
295A ALA* 1.3 75.0 - - - +
297A ARG* 1.3 63.5 + - - +
300A PHE* 3.2 57.8 + + + +
453A PHE* 3.7 11.8 - + + -
483A ARG* 3.6 23.7 + - - -
534A GLU* 3.8 27.5 + - - +
537A LEU* 3.9 25.6 - - + +
538A GLY* 3.5 32.2 - - - -
541A THR* 4.3 13.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A SER 5.6 0.6 + - - -
293A ALA* 3.0 42.1 + - - +
294A ARG* 3.0 21.5 + - - +
296A HIS* 1.3 77.5 - - - +
298A GLU* 1.3 63.9 + - + +
300A PHE 3.8 12.3 - - - +
534A GLU* 3.9 31.9 - - + +
535A GLU* 4.5 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ARG* 2.8 49.5 + - + +
295A ALA* 3.9 8.5 - - - +
297A ARG* 1.3 80.6 - - + +
299A ILE* 1.3 67.0 + - + +
300A PHE 3.7 1.6 + - - -
456A HIS* 5.0 10.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ALA* 2.9 25.0 + - + +
298A GLU* 1.3 82.7 - - + +
300A PHE* 1.3 64.2 + - + +
449A GLU* 3.3 54.9 - - + +
452A GLU* 3.6 21.3 - - + -
453A PHE* 3.4 32.8 - - + +
456A HIS* 3.7 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A HIS* 3.2 47.1 + + + +
297A ARG* 3.8 13.3 - - - +
298A GLU 4.8 1.3 - - - -
299A ILE* 1.3 82.5 - - + +
446A ALA 5.2 0.2 - - - -
449A GLU* 3.8 38.6 - - + -
450A VAL* 4.3 13.7 - - + -
453A PHE* 3.6 45.1 - + + -
479A VAL* 5.0 0.4 - - + -
480A LEU* 6.2 0.2 - - + -
483A ARG* 3.4 59.6 + - + +
534A GLU* 5.7 1.0 - - - +
541A THR* 4.8 4.0 - - + -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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