Contacts of the strand formed by residues 397 - 405 (chain B) in PDB entry 4WIK
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 ILE 397 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B GLU* 3.9 33.0 - - + +
391B PHE* 3.7 25.8 - - + +
392B SER* 4.0 5.2 - - - +
395B GLY 3.5 1.0 + - - -
396B PRO* 1.4 70.9 - - - +
398B GLU* 1.3 63.0 + - - +
399B ARG* 3.8 23.3 - - - +
400B ALA* 3.9 11.7 - - + -
416B VAL* 4.0 19.1 - - + -
417B GLU 3.9 4.0 - - - +
418B PHE* 3.6 32.3 - - + -
419B ALA* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B PRO 3.7 3.8 + - - -
397B ILE* 1.3 75.2 - - - +
399B ARG* 1.4 68.6 + - - +
417B GLU* 2.8 42.6 + - - +
418B PHE 4.0 15.7 - - - +
419B ALA* 4.2 9.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A ASP* 3.5 22.0 + - - -
456A GLU* 4.0 29.2 + - - +
388B GLU* 5.6 1.1 - - - -
397B ILE* 3.5 5.5 - - - +
398B GLU* 1.4 85.1 - - - +
400B ALA* 1.3 60.6 + - - +
401B VAL* 4.0 22.2 - - - +
415B ILE* 3.9 13.8 - - - +
416B VAL* 3.6 0.5 - - - -
417B GLU* 2.6 62.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B ASN* 3.5 11.7 - - - +
387B LEU* 4.1 4.7 - - + -
388B GLU* 3.3 53.6 + - + +
397B ILE* 3.9 6.8 - - + +
399B ARG* 1.3 79.1 + - - +
401B VAL* 1.3 62.4 + - - +
415B ILE 3.3 5.2 - - - -
416B VAL* 3.8 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A ASP* 3.3 30.7 - - - +
456A GLU 4.1 15.9 - - - +
457A ASP 4.1 11.9 - - - +
458A GLY 4.1 0.7 - - - +
384B ASN* 3.7 14.8 - - - +
387B LEU* 3.4 6.5 - - - +
399B ARG* 4.0 19.5 - - - +
400B ALA* 1.3 74.5 - - - +
402B VAL* 1.3 75.2 + - - +
403B ILE* 5.0 1.6 - - + +
414B GLY* 3.4 2.8 - - - -
415B ILE* 2.9 53.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A ASP 3.8 2.3 - - - +
458A GLY* 3.3 21.5 - - - -
459A LEU* 4.2 8.1 - - + +
378B LEU* 4.8 7.2 - - + -
382B VAL* 3.6 18.2 - - + +
383B SER* 3.5 35.7 - - - +
384B ASN* 3.0 13.8 + - - +
387B LEU* 4.6 7.9 - - + -
401B VAL* 1.3 79.9 - - - +
403B ILE* 1.3 70.8 + - - +
404B VAL* 4.0 9.4 - - + -
410B SER* 3.7 23.3 - - - +
413B LYS 4.0 8.5 - - - +
414B GLY* 4.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A LEU* 3.8 32.3 - - + -
454A ASP 3.6 8.7 - - - +
455A ASP* 5.0 9.0 - - + -
374B SER* 5.5 1.6 - - - +
401B VAL* 5.1 2.5 - - + -
402B VAL* 1.3 74.9 - - - +
404B VAL* 1.3 63.5 + - - +
411B THR* 2.6 45.0 + - + +
413B LYS* 3.1 20.6 + - + +
414B GLY* 3.7 28.3 - - - +
415B ILE* 3.8 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A LEU* 3.6 1.8 - - - -
454A ASP* 2.7 57.8 + - + +
458A GLY* 3.5 21.1 - - - +
459A LEU* 3.7 32.3 - - + +
402B VAL* 3.9 7.6 - - + +
403B ILE* 1.3 80.2 - - - +
405B ASP* 1.3 63.3 + - - +
408B GLY* 3.9 13.9 - - - +
409B ARG 3.2 15.5 - - - +
410B SER* 4.0 3.6 - - - -
411B THR* 3.8 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A GLN 5.3 0.2 - - - +
453A LEU* 3.9 22.7 - - + +
454A ASP* 5.0 3.2 - - - +
404B VAL* 1.3 79.5 - - - +
406B ASP* 1.4 62.8 + - - +
407B ARG* 3.0 24.3 + - - +
408B GLY* 2.9 21.3 + - - -
409B ARG* 2.9 71.7 + - - +
410B SER 4.5 4.5 - - - +
411B THR* 3.8 6.0 - - + +
----------------------------------------------------------
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