Contacts of the strand formed by residues 407 - 411 (chain C) in PDB entry 4IG9
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 MET 407 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C PHE* 4.0 0.2 - - - -
369C ALA* 3.6 21.3 - - + +
371C CYS* 3.7 24.5 - - - +
376C TYR* 3.2 23.8 - - + +
378C VAL* 3.7 29.2 - - + -
383C VAL* 4.0 22.5 - - + +
387C ILE* 6.0 0.2 - - - +
393C PRO* 3.3 25.5 + - + +
394C ARG 3.4 25.1 - - - +
395C CYS* 4.0 15.5 - - - -
396C PRO* 4.4 5.6 - - + -
405C ALA 4.2 0.2 + - - -
406C ILE* 1.3 72.9 - - - +
408C LYS* 1.3 61.4 + - - +
409C PRO* 3.7 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 408 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C ILE* 4.4 0.4 - - + -
302C PHE* 3.7 19.1 - - + -
309C PHE* 5.1 0.2 - - + -
369C ALA* 3.9 0.7 - - - -
370C SER* 2.6 45.9 + - - +
372C LEU* 3.7 22.2 - - + -
406C ILE* 3.2 18.0 + - + +
407C MET* 1.3 71.5 - - - +
409C PRO* 1.3 89.8 + - + +
410C GLU* 4.7 1.6 - - - +
411C ILE* 3.4 20.2 + - - +
413C PHE* 3.7 31.0 - - + -
416C GLU* 3.7 21.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 409 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C PHE* 4.0 13.7 - - + -
310C PHE* 3.8 18.6 - - + -
317C TYR* 5.6 0.9 - - + -
365C SER 4.5 0.2 - - - +
366C PHE* 3.7 35.4 - - + -
368C THR 3.5 10.1 - - - +
369C ALA* 3.7 8.7 - - + -
383C VAL* 5.8 1.1 - - + -
387C ILE* 4.5 12.6 - - + -
407C MET 3.7 6.7 - - - +
408C LYS* 1.3 110.6 + - + +
410C GLU* 1.3 53.9 - - - +
411C ILE* 2.7 23.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 410 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C GLY* 3.0 8.0 - - - -
365C SER* 2.4 48.2 + - - +
368C THR* 2.8 45.3 + - - +
369C ALA* 4.1 5.6 - - - +
370C SER* 4.5 9.4 - - - +
377C LYS* 3.6 21.1 - - + +
408C LYS* 4.9 1.8 - - - +
409C PRO* 1.3 67.1 - - - +
411C ILE* 1.3 53.5 + - - +
412C VAL* 5.8 0.2 - - - -
419C PRO* 6.1 2.4 - - - +
421C GLN* 5.7 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 411 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C PHE* 4.5 16.6 - - + -
309C PHE* 4.2 16.6 - - + -
347C ILE* 3.9 14.8 - - + -
363C HIS 4.0 4.9 - - - +
364C GLY 3.9 3.6 - - - -
365C SER* 3.6 34.5 - - - +
366C PHE* 3.9 18.2 - - + -
408C LYS* 3.4 12.2 + - - +
409C PRO* 2.7 20.3 + - + +
410C GLU* 1.3 73.1 - - - +
412C VAL* 1.3 66.9 + - - +
413C PHE* 3.2 37.1 + - + -
416C GLU* 3.3 10.2 - - - +
----------------------------------------------------------
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