Contacts of the helix formed by residues 383 - 396 (chain B) in PDB entry 4XX1
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 383 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B ILE* 3.2 30.1 - - - +
379B ASN* 2.6 22.5 + - - -
382B PHE* 1.3 71.5 - - - +
384B ASN* 1.3 65.0 + - - +
385B LEU* 3.3 13.5 + - - +
386B THR* 2.6 40.4 + - - -
387B LEU* 3.1 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B PHE 3.2 6.0 + - - +
383B SER* 1.3 73.0 + - - +
385B LEU* 1.3 61.4 + - - +
387B LEU* 3.7 16.1 + - + +
388B GLU* 3.4 20.6 + - - +
503B NAG 1.5 70.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B LEU* 4.3 16.2 - - + -
373B HIS 4.6 8.7 - - - +
375B ILE* 3.7 30.5 - - + -
383B SER* 3.0 10.6 + - - +
384B ASN* 1.3 76.8 - - - +
386B THR* 1.3 66.6 + - + +
388B GLU* 3.3 21.2 + - + +
389B HIS* 3.2 41.9 + - + +
503B NAG 5.9 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LEU* 6.5 1.1 - - - -
314B LEU* 5.4 4.4 - - - +
372B LEU* 3.5 30.3 - - + -
375B ILE* 4.3 6.5 - - + -
380B MET* 2.7 35.9 + - + +
381B VAL* 4.6 1.7 - - - -
383B SER* 2.6 32.6 + - - +
385B LEU* 1.3 73.0 - - + +
387B LEU* 1.3 70.3 + - - +
389B HIS* 2.9 20.0 + - - +
390B ILE* 3.0 21.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B THR* 4.2 22.0 - - + -
124B LEU* 3.6 40.6 - - + -
127B ASN* 4.1 28.2 + - + +
381B VAL 4.4 11.0 - - - +
382B PHE 4.4 3.4 - - - +
383B SER 3.1 15.5 + - - +
384B ASN* 3.8 18.4 - - + +
385B LEU 3.3 0.2 - - - -
386B THR* 1.3 83.1 + - - +
388B GLU* 1.3 62.6 + - - +
390B ILE* 3.4 7.1 + - + +
391B ASN* 3.1 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B ASN* 3.4 10.8 + - - +
385B LEU* 3.3 19.0 + - - +
386B THR 3.1 0.6 - - - -
387B LEU* 1.3 77.7 - - - +
389B HIS* 1.3 69.1 + - + +
390B ILE 3.3 0.2 + - - -
391B ASN* 3.4 10.5 + - - +
392B ALA* 3.2 22.5 + - + +
503B NAG 3.8 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B LEU* 4.6 15.3 - - + -
370B LEU* 3.4 32.5 - - + +
371B PRO 5.1 1.8 + - - -
372B LEU* 3.9 22.5 - - + +
385B LEU* 3.2 41.9 + - + +
386B THR* 2.9 11.0 + - - +
388B GLU* 1.3 83.0 - - + +
390B ILE* 1.3 63.6 + - - +
392B ALA* 3.4 12.1 + - - +
393B ILE* 3.3 20.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 4.1 23.1 - - + -
127B ASN* 5.4 0.2 - - - +
128B LEU* 4.5 12.6 - - + -
178B ILE* 4.5 17.5 - - + -
207B ILE* 5.1 5.8 - - + -
209B LEU* 4.5 25.4 - - + -
314B LEU* 4.4 16.4 - - + -
386B THR* 3.0 20.6 + - - +
387B LEU* 3.8 9.6 - - + +
389B HIS* 1.3 73.1 - - - +
391B ASN* 1.3 67.9 + - - +
393B ILE* 2.9 19.6 + - - +
394B LEU* 3.2 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ASN* 2.6 41.8 + - - +
128B LEU* 4.5 5.7 - - - +
131B ASN* 4.0 22.6 + - - +
387B LEU* 3.1 22.4 + - - +
388B GLU* 3.6 8.7 - - - +
390B ILE* 1.3 75.8 - - - +
392B ALA* 1.3 62.4 + - - +
394B LEU* 4.9 2.4 - - - +
395B LEU* 3.1 43.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B GLU* 3.2 10.3 + - + +
389B HIS* 3.6 11.9 - - - +
390B ILE 3.1 0.6 - - - -
391B ASN* 1.3 79.2 - - - +
393B ILE* 1.3 64.3 + - + +
395B LEU* 5.3 0.2 - - - -
396B GLY* 3.3 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 393 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ARG* 3.6 9.9 + - - -
176B PHE* 3.5 29.0 - - + -
207B ILE* 4.0 20.0 - - + -
312B TYR* 3.4 59.8 + - + +
314B LEU* 5.1 6.3 - - + -
370B LEU* 5.5 9.9 - - + -
389B HIS 3.3 16.6 - - - +
390B ILE* 2.9 10.5 + - - +
392B ALA* 1.3 78.9 - - + +
394B LEU* 1.3 64.7 + - - +
395B LEU 3.4 0.5 + - - -
396B GLY 3.8 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ARG* 2.6 39.4 + - + +
25B VAL* 4.0 18.2 - - + -
128B LEU* 4.0 27.1 - - + -
133B TYR* 3.5 30.5 + - + +
176B PHE* 3.4 30.1 - - + -
178B ILE* 4.5 5.8 - - + -
207B ILE* 3.9 17.9 - - + -
390B ILE* 3.2 22.3 + - + +
391B ASN* 4.3 3.4 - - - +
393B ILE* 1.3 75.7 - - - +
395B LEU* 1.3 62.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B THR* 5.0 10.1 - - + -
23B ARG* 3.6 7.8 + - - +
131B ASN* 3.3 44.6 - - + +
133B TYR* 4.2 20.6 - - + +
391B ASN* 3.1 28.6 + - + +
394B LEU* 1.3 92.0 - - + +
396B GLY* 1.3 65.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ARG* 3.5 13.7 + - - -
392B ALA* 3.3 22.6 + - - +
393B ILE 3.8 3.8 - - - +
395B LEU* 1.3 83.7 - - - +
----------------------------------------------------------
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