Contacts of the strand formed by residues 351 - 358 (chain B) in PDB entry 3IW4
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 351 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LYS* 3.4 1.5 - - - -
348B GLY 2.6 39.8 + - - -
349B SER 3.0 4.8 + - - -
350B PHE* 1.3 82.5 - - - +
352B LYS* 1.3 59.9 + - - -
368B LYS* 4.6 0.2 - - - -
370B LEU* 4.1 20.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B VAL* 4.3 15.7 - - + -
346B GLY 3.5 8.3 - - - +
347B LYS* 3.1 37.0 - - + +
350B PHE 4.0 0.6 + - - -
351B GLY* 1.3 71.6 - - - -
353B VAL* 1.3 62.1 + - - +
354B MET* 4.1 25.1 - - + -
367B ILE 3.5 2.3 - - - +
368B LYS* 3.6 0.4 - - - -
369B ILE* 3.0 48.3 + - + +
637B LEU* 6.3 2.0 - - + -
638B TPO 5.6 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B VAL* 3.5 4.7 - - - +
345B LEU* 2.7 29.0 + - + -
346B GLY 2.9 18.2 + - - +
350B PHE* 3.5 28.9 - - + +
352B LYS* 1.3 74.8 - - - +
354B MET* 1.3 58.6 + - - +
366B ALA* 3.7 27.8 - - + -
367B ILE 3.5 11.0 - - - +
368B LYS* 4.3 7.4 - - + +
901B LW4 3.8 51.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B PHE* 3.7 30.1 - - + -
343B MET 3.4 26.0 - - - +
344B VAL* 3.9 9.2 - - + -
345B LEU* 4.2 4.0 - - - -
352B LYS* 4.1 20.4 - - + -
353B VAL* 1.3 76.3 - - - +
355B LEU* 1.3 72.6 + - - +
356B ALA* 3.6 0.7 + - + -
366B ALA* 3.4 4.2 - - - -
367B ILE* 2.9 39.9 + - + +
369B ILE* 3.9 24.5 - - + -
635B PRO* 3.7 27.8 - - + -
636B VAL 5.9 1.8 - - - +
637B LEU* 5.6 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B PHE* 3.7 2.9 - - - -
342B LEU* 2.8 41.7 + - + -
343B MET* 2.5 52.4 + - + +
345B LEU* 3.8 15.8 - - + +
354B MET* 1.3 72.6 - - - +
356B ALA* 1.3 68.2 + - - +
364B LEU* 4.2 15.0 - - + -
365B TYR 3.5 9.9 - - - +
419B TYR* 3.9 47.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B PHE* 4.3 7.9 - - + -
340B ASN 3.3 13.5 - - - +
341B PHE* 4.3 9.6 - - + -
342B LEU* 4.0 5.4 - - - -
354B MET 4.5 0.7 - - - +
355B LEU* 1.3 77.6 - - - +
357B ASP* 1.3 59.7 + - - +
364B LEU* 3.3 3.2 - - - +
365B TYR* 2.7 45.8 + - - +
367B ILE* 3.6 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B PHE* 3.5 5.5 - - - -
340B ASN* 3.0 51.1 + - - +
342B LEU* 3.7 17.2 - - + +
356B ALA* 1.3 74.1 - - - +
358B ARG* 1.3 82.5 + - - +
359B LYS* 4.3 3.0 + - - -
360B GLY 4.9 0.9 + - - -
361B THR 3.9 5.2 - - - +
362B GLU* 4.7 4.0 - - - +
363B GLU 3.1 15.0 - - - +
364B LEU* 3.2 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ASP* 4.1 25.8 + - - +
333B ARG 4.5 3.6 + - - -
334B VAL* 3.5 30.6 - - - +
338B ASP* 3.6 15.1 - - + +
339B PHE* 4.0 13.6 - - + -
356B ALA 4.3 0.4 + - - -
357B ASP* 1.3 79.3 - - - +
359B LYS* 1.3 68.9 + - - +
360B GLY 3.3 0.5 + - - -
361B THR* 2.7 44.4 - - + +
363B GLU* 3.1 30.8 + - + -
365B TYR* 4.0 22.2 + - + -
404B HIS* 5.2 3.7 + - - -
665B HIS* 5.7 2.4 - - - -
----------------------------------------------------------
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