Contacts of the strand formed by residues 306 - 310 (chain G) in PDB entry 4KYI
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 306 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G HIS* 4.3 0.2 - - - -
37G GLY* 3.7 5.6 - - - -
39G VAL* 3.7 28.3 - - + -
297G GLU* 6.4 0.2 - - - -
298G ILE* 4.1 22.7 - - + +
301G LEU* 3.6 31.6 - - + +
302G ASP 3.4 19.3 - - - +
303G ARG* 3.4 8.4 + - - +
304G GLU 3.6 0.8 - - - -
305G GLU* 1.3 82.9 - - - +
307G LEU* 1.3 64.0 - - - +
308G CYS* 3.5 10.4 + - - -
370G ASN* 3.2 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 307 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G HIS* 3.4 42.8 - - + +
37G GLY 3.0 13.4 + - - +
38G LEU* 3.5 19.5 - - + +
39G VAL* 3.0 25.8 + - - +
57G LEU* 4.0 27.6 - - + -
62G LYS* 4.5 13.2 - - + +
66G LEU* 5.6 2.5 - - + -
305G GLU 4.2 0.2 - - - -
306G VAL* 1.3 70.7 - - - +
308G CYS* 1.3 62.3 + - - +
370G ASN* 3.6 18.8 - - + +
372G ILE* 5.2 7.6 - - + -
405G LEU* 4.3 8.5 - - + -
406G LEU* 4.8 6.3 - - + -
409G HIS* 4.0 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 308 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G VAL* 3.7 20.6 - - - -
295G MET* 3.4 29.4 - - - -
296G PRO 5.4 0.7 - - - -
303G ARG* 5.8 3.8 - - - -
306G VAL* 4.0 15.9 - - - -
307G LEU* 1.3 73.5 - - - +
309G VAL* 1.3 62.4 + - - +
310G LYS 4.3 0.4 - - - -
370G ASN* 2.7 20.5 + - - +
371G MET* 3.5 16.4 - - + +
372G ILE* 2.8 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 309 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G LEU* 4.5 11.9 - - + -
39G VAL 3.0 8.1 + - - +
40G LEU* 3.6 20.3 - - + -
41G SER* 2.3 36.7 + - - -
50G TYR* 4.1 25.3 + - + -
53G MET* 4.5 11.2 - - + -
295G MET* 4.3 1.5 - - - +
307G LEU 5.0 0.2 - - - -
308G CYS* 1.3 79.5 - - - +
310G LYS* 1.3 57.8 + - - +
311G ALA 4.3 0.2 + - - -
372G ILE* 3.3 33.7 - - + +
374G ILE* 4.1 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 310 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G SER* 3.1 19.1 - - - +
42G GLY 5.6 2.4 + - - +
293G ASP* 2.7 37.7 + - + +
295G MET* 5.6 3.8 - - + -
308G CYS 4.3 0.4 - - - -
309G VAL* 1.3 76.4 - - - +
311G ALA* 1.3 57.1 + - - +
312G GLU* 3.4 34.6 + - - +
371G MET* 4.6 8.7 - - - -
372G ILE 2.8 8.9 + - - -
373G TYR* 3.3 31.9 - - + -
374G ILE* 2.8 31.7 + - - +
----------------------------------------------------------
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