Contacts of the strand formed by residues 403 - 408 (chain A) 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 LEU 403 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A LYS 4.6 1.6 - - - +
391A LEU* 3.7 49.8 - - + +
392A ALA* 4.1 4.9 - - + +
396A LYS* 3.6 9.3 - - - +
401A THR 3.6 0.2 + - - -
402A GLN* 1.3 72.8 - - - +
404A HIS* 1.3 59.2 + - - +
405A SER* 3.4 24.5 - - - +
406A CYS* 4.3 17.3 - - - -
415A PHE* 4.7 1.3 - - - -
416A VAL 3.4 19.7 - - - +
417A MET* 3.8 15.5 - - + -
658A TYR* 4.2 22.4 - - + -
660A ASN* 3.1 21.4 + - + +
663A PHE* 3.1 13.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ASP* 3.4 34.0 + - + +
334A VAL* 3.7 13.3 - - + +
358A ARG* 3.3 26.9 + - - -
365A TYR* 3.3 27.8 - + + -
402A GLN 4.0 0.4 + - - -
403A LEU* 1.3 74.1 - - - +
405A SER* 1.3 92.9 + - - +
416A VAL* 2.6 32.6 + - + +
659A VAL* 4.1 1.9 - - + +
660A ASN* 3.0 23.9 + - - +
663A PHE* 3.5 31.6 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A VAL* 3.6 14.4 - - - +
403A LEU* 3.4 11.7 - - - +
404A HIS* 1.3 107.7 - - - +
406A CYS* 1.3 64.7 + - - +
407A PHE* 5.4 1.6 - - - -
416A VAL* 2.8 33.3 + - - +
658A TYR 3.2 15.7 - - - -
659A VAL* 3.7 19.1 - - - +
660A ASN 4.5 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A LYS* 3.8 26.5 - - - -
403A LEU* 4.3 13.7 - - - -
405A SER* 1.3 79.0 - - - +
407A PHE* 1.3 70.1 + - - +
414A TYR 3.4 5.2 - - - -
415A PHE* 4.1 17.3 - - - -
656A PHE* 3.4 34.5 - - + +
657A SEP 3.4 4.4 - - - +
658A TYR* 2.8 27.8 + - - +
659A VAL* 4.9 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A VAL* 3.8 25.8 - - + +
335A LYS* 3.7 10.5 - - + -
336A LEU* 3.7 35.7 - - + -
339A PHE* 4.8 4.5 - + - -
367A ILE* 5.9 0.9 - - + -
405A SER* 5.4 1.1 - - - -
406A CYS* 1.3 81.2 - - - +
408A GLN* 1.3 69.6 + - - +
409A THR* 5.0 1.3 - - - -
414A TYR* 3.0 64.3 + + + +
416A VAL* 3.9 26.2 - - + -
656A PHE* 3.4 6.6 - - - -
657A SEP 3.3 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A LYS* 2.9 23.9 + - - +
407A PHE* 1.3 84.8 - - - +
409A THR* 1.3 66.1 + - - +
412A ARG 3.3 12.6 - - - +
413A LEU* 3.8 15.7 - - + +
650A GLN* 4.5 3.8 - - - +
653A PHE* 3.6 33.5 + - - +
655A GLY 5.2 1.2 - - - +
656A PHE* 4.0 10.3 - - + +
657A SEP 3.1 35.1 + - - +
----------------------------------------------------------
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