Contacts of the strand formed by residues 409 - 414 (chain C) in PDB entry 6T8G
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 VAL 409 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C ILE* 2.9 40.3 + - + +
372C PRO* 4.3 15.0 - - + -
377C LYS 6.1 0.2 - - - +
378C VAL* 4.2 24.5 - - + -
381C ILE* 4.8 16.8 - - + -
399C VAL* 4.7 6.7 - - + -
400C VAL 3.4 16.6 - - - +
401C GLU* 4.5 6.5 - - - +
402C VAL 5.7 0.2 - - - +
408C THR* 1.3 81.7 - - - +
410C GLY* 1.3 66.2 + - - +
411C ILE* 3.8 1.1 + - + +
390D ARG* 3.8 27.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 410 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C ARG* 4.6 9.2 - - - -
368C PHE 3.8 11.0 - - - -
369C GLU* 5.3 0.2 - - - -
399C VAL* 3.5 3.1 - - - +
400C VAL* 2.6 59.0 + - - +
402C VAL 5.4 0.2 - - - +
403C ILE* 5.5 4.2 - - - +
408C THR* 4.2 1.7 + - - -
409C VAL* 1.3 73.7 - - - +
411C ILE* 1.3 65.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
343C LEU* 4.4 11.7 - - + -
347C LEU* 4.9 2.5 - - + -
366C THR 3.6 1.4 - - - +
367C ARG* 3.9 0.4 - - - +
368C PHE* 3.0 40.7 + - + +
370C ILE* 3.6 29.2 - - + -
381C ILE* 4.2 20.0 - - + -
388C LEU* 4.5 19.3 - - + -
397C VAL* 3.7 22.7 - - + -
398C ARG 3.4 7.9 - - - +
399C VAL* 4.4 11.4 - - + -
409C VAL* 3.8 2.1 + - + +
410C GLY* 1.3 78.6 - - - +
412C GLU* 1.3 63.5 + - - +
413C ILE* 3.9 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 412 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C ILE* 3.8 19.7 - - + +
366C THR 3.5 5.4 - - - -
367C ARG* 4.1 13.8 + - - -
397C VAL* 3.3 13.6 - - - +
398C ARG* 3.0 54.8 + - + +
400C VAL* 4.0 11.9 - - + +
411C ILE* 1.3 74.7 - - - +
413C ILE* 1.3 63.8 - - - +
414C PRO* 3.6 3.6 - - - +
447C ILE* 3.7 22.2 - - - +
690C ARG* 2.4 44.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 413 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C MET* 4.3 23.1 - - + -
343C LEU* 3.7 25.1 - - + -
365C ILE* 3.3 4.4 - - - +
366C THR* 3.0 32.0 + - - +
368C PHE* 3.5 31.2 - - + -
392C LEU* 4.3 15.3 - - + -
394C VAL* 4.1 9.9 - - + -
397C VAL* 3.7 7.6 - - + -
411C ILE* 3.9 17.2 - - + -
412C GLU* 1.3 70.6 - - - +
414C PRO* 1.3 84.0 - - + +
415C ASN* 3.4 1.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 414 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C MET* 6.1 0.3 - - - +
365C ILE* 4.0 10.3 - - + -
394C VAL* 3.4 34.6 - - + +
395C ILE* 4.7 2.5 - - + +
396C SER 3.3 27.4 - - - +
397C VAL* 3.9 7.9 - - + -
412C GLU 3.6 7.4 - - - +
413C ILE* 1.3 98.3 - - + +
415C ASN* 1.3 61.3 + - - +
416C GLU* 4.0 10.5 + - - +
673C LEU* 3.7 26.5 - - + -
----------------------------------------------------------
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