Contacts of the helix formed by residues 394 - 408 (chain B) in PDB entry 3W8I
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 GLY 394 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B VAL* 6.4 0.2 - - - +
389B GLU* 2.7 16.7 + - - -
393B PRO* 1.3 72.5 - - - +
395B ILE* 1.3 61.1 + - - +
396B THR 3.2 2.9 - - - -
397B ASP* 3.3 22.3 + - - +
398B LYS* 3.1 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.9 32.1 - - + +
36A VAL* 4.6 8.1 - - + -
37A ASN 4.5 1.3 - - - +
40A ALA* 3.6 25.6 - - + -
41A ALA 4.1 7.0 - - - +
44A LEU* 3.9 23.0 - - + +
388B ALA* 3.7 18.6 - - + +
389B GLU* 3.7 7.6 - - - +
392B CYS* 3.2 28.9 + - + +
393B PRO 3.4 0.8 + - - -
394B GLY* 1.3 76.9 - - - +
396B THR* 1.3 66.0 + - - +
398B LYS* 3.4 7.5 + - - +
399B MET* 2.9 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 6.0 1.4 - - - +
351B SER* 4.5 1.1 - - - -
352B CYS* 4.1 4.3 - - + -
353B LEU* 3.8 21.1 - - - +
357B ILE* 3.7 33.0 - - + -
385B ILE* 3.8 22.1 + - + +
389B GLU* 2.6 29.9 + - - +
395B ILE* 1.3 77.4 - - - +
397B ASP* 1.3 60.6 + - - +
399B MET* 3.3 11.8 + - + +
400B VAL* 2.9 30.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B LEU 4.1 4.8 - - - +
351B SER* 3.7 18.3 + - - -
352B CYS* 2.9 40.9 + - - -
394B GLY* 3.3 21.4 + - - +
396B THR* 1.3 79.3 - - - +
398B LYS* 1.3 56.9 + - + +
400B VAL* 3.8 1.7 - - - +
401B LYS* 2.9 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.9 12.8 - - + -
36A VAL* 3.8 42.2 - - + -
393B PRO 5.6 1.6 - - - -
394B GLY* 3.1 22.9 + - - +
395B ILE* 3.7 6.1 - - - +
397B ASP* 1.3 76.1 - - + +
399B MET* 1.3 65.4 + - - +
401B LYS* 3.9 5.3 - - - +
402B LYS* 2.9 46.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A MET* 4.3 13.0 - - + -
29A VAL* 3.8 19.8 - - + +
30A PHE* 4.4 3.6 - - + -
33A LEU* 3.8 16.9 - - + +
44A LEU* 4.0 24.9 - - + -
48A PHE* 4.1 27.6 - - + -
66A ILE* 5.4 4.7 - - + -
357B ILE* 4.4 16.4 - - + -
385B ILE* 4.7 11.0 - - + -
395B ILE 2.9 19.1 + - - +
396B THR* 3.3 24.4 + - + +
398B LYS* 1.3 75.3 - - - +
400B VAL* 1.3 60.7 + - + +
403B LEU* 2.9 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ILE* 4.3 20.9 - - + -
70A LYS* 3.6 32.1 - - + +
352B CYS* 3.8 26.9 - - + -
356B ILE* 4.9 3.8 - - + -
357B ILE* 4.5 14.4 - - + -
396B THR* 2.9 27.8 + - + +
397B ASP 3.8 3.4 - - - +
399B MET* 1.3 81.3 - - + +
401B LYS* 1.3 57.4 + - - +
403B LEU* 3.2 10.2 - - + +
404B ILE* 2.9 30.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B ASP 2.9 19.8 + - - +
398B LYS* 3.9 5.8 - - - +
400B VAL* 1.3 78.4 - - - +
402B LYS* 1.3 60.7 + - + +
404B ILE* 3.2 16.9 - - + +
405B GLU* 2.9 56.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 4.2 15.9 - - + -
32A GLU* 3.2 41.2 + - + +
33A LEU* 4.0 19.1 - - + -
35A ARG* 4.1 17.4 - - - +
36A VAL* 6.1 0.9 - - - -
398B LYS* 2.9 41.7 + - - +
399B MET 4.1 1.8 - - - +
401B LYS* 1.3 76.3 - - - +
403B LEU* 1.3 67.4 + - - +
405B GLU* 3.0 18.5 + - - +
406B LYS* 3.0 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL* 3.7 17.7 - - + -
26A MET* 4.0 24.5 - - + -
29A VAL* 4.2 9.8 - - + +
63A ILE* 4.1 15.7 - - + +
66A ILE* 4.0 40.8 - - + -
67A LEU* 5.5 2.0 - - + -
399B MET* 2.9 22.6 + - + +
400B VAL* 3.2 7.9 - - - +
402B LYS* 1.3 75.1 - - - +
404B ILE* 1.3 58.9 + - + +
406B LYS* 3.1 18.3 + - - +
407B PHE* 3.3 40.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ILE* 4.9 5.6 - - + -
67A LEU* 3.8 28.9 - - + -
70A LYS* 3.7 42.4 - - + +
72A VAL* 4.0 19.5 - - + +
400B VAL* 2.9 17.9 + - + +
401B LYS* 3.2 25.8 - - + +
403B LEU* 1.3 73.9 - - + +
405B GLU* 1.3 55.4 + - + +
407B PHE* 3.1 1.0 + - - +
408B GLN* 2.6 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B LYS* 2.9 52.5 + - + +
402B LYS* 3.0 28.2 + - - +
404B ILE* 1.3 78.2 - - + +
406B LYS* 1.3 61.3 + - - +
408B GLN* 3.5 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA 3.4 13.1 + - - -
25A VAL* 3.7 19.5 + - + +
28A PRO* 3.4 36.6 - - - +
29A VAL* 4.1 8.5 - - + -
32A GLU* 5.5 5.6 - - - +
83A MET* 3.6 40.1 + - + +
86A ASP* 5.8 1.6 + - - -
402B LYS* 3.0 20.6 + - + +
403B LEU 3.1 10.0 + - - +
405B GLU* 1.3 81.2 - - - +
407B PHE* 1.3 64.3 + - + +
408B GLN* 3.9 10.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL* 3.6 31.0 - - + -
63A ILE* 3.7 20.6 - - + -
67A LEU* 3.9 32.1 - - + -
72A VAL* 4.5 2.5 - - + -
74A VAL* 4.2 23.4 - - + +
76A PHE* 3.8 29.4 - + - -
79A SER* 3.5 33.6 + - - -
80A LEU 4.6 1.8 - - - -
83A MET* 4.0 12.6 - - + -
403B LEU* 3.3 23.1 - - + -
404B ILE 3.1 3.2 + - - +
406B LYS* 1.3 77.6 - - + +
408B GLN* 1.3 74.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 408 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A VAL* 3.7 27.5 - - - +
74A VAL* 6.2 0.2 - - - -
404B ILE* 2.6 22.7 + - - +
405B GLU* 3.5 20.1 + - - +
406B LYS* 3.9 9.2 + - - +
407B PHE* 1.3 80.3 - - - +
----------------------------------------------------------
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