Contacts of the strand formed by residues 305 - 313 (chain A) in PDB entry 3KYS
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 305 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A LEU* 3.7 10.8 - - + -
297A TYR* 5.4 0.7 - - + -
303A MET* 3.5 3.8 + - + +
304A THR* 1.3 75.0 - - - +
306A THR* 1.3 60.7 + - - +
307A CYS* 3.8 14.1 - - - -
323A GLU 4.0 0.2 - - - +
324A THR* 3.5 3.3 - - - +
325A GLU* 2.6 51.2 + - + +
336A TYR* 3.6 39.9 - - + +
376A VAL* 3.8 20.2 - - + -
377A THR 3.6 1.6 - - - -
385A LEU* 3.6 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A THR 4.2 0.6 + - - -
305A VAL* 1.3 73.8 + - - +
307A CYS* 1.3 65.1 + - - +
308A SER* 4.8 3.6 - - - +
322A VAL* 3.8 28.5 - - + -
323A GLU 3.4 3.1 - - - -
324A THR* 3.6 13.7 + - - +
375A VAL 3.8 1.6 - - - +
376A VAL* 3.5 0.9 - - - -
377A THR* 2.7 50.1 + - - -
379A ARG* 3.5 34.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A TYR* 3.8 31.9 - - - +
305A VAL* 3.8 23.8 - - - -
306A THR* 1.3 73.1 - - - +
308A SER* 1.3 59.6 + - - +
309A THR* 4.1 2.0 + - - +
321A LYS 3.6 2.1 - - - +
322A VAL* 3.5 0.7 - - - -
323A GLU* 2.6 56.0 + - + +
325A GLU* 4.9 0.9 - - - -
338A ILE* 4.1 17.3 - - + -
374A LEU* 4.8 5.6 - - + -
375A VAL 3.7 3.8 - - - -
376A VAL* 4.0 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A THR* 4.0 5.5 + - - -
307A CYS* 1.3 72.9 - - - +
309A THR* 1.3 61.6 + - - +
310A LYS* 3.8 10.2 - - - +
320A GLU* 3.1 34.2 + - - +
321A LYS 3.4 4.7 - - - -
322A VAL* 4.0 8.0 - - - +
373A LEU 3.6 2.4 - - - +
374A LEU* 3.5 4.2 - - - +
375A VAL* 2.8 46.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A PHE* 6.2 4.3 - - + -
293A VAL* 6.4 0.7 - - + -
307A CYS* 4.8 3.8 + - - +
308A SER* 1.3 71.7 - - - +
310A LYS* 1.3 60.6 + - - +
311A VAL* 4.2 0.8 + - + -
319A VAL 3.8 1.4 - - - +
320A GLU* 3.5 0.5 - - - -
321A LYS* 2.7 46.4 + - - +
323A GLU* 4.7 10.2 + - - +
344A P1L 3.9 40.1 - - + +
372A ILE* 3.9 18.4 - - + -
373A LEU 3.7 2.0 - - - -
374A LEU* 3.5 22.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A PRO* 3.7 17.9 - - - +
256A GLY 4.0 15.6 + - - -
257A GLY* 5.1 1.4 - - - -
308A SER* 3.8 20.2 - - - +
309A THR* 1.3 77.8 - - - +
311A VAL* 1.3 62.6 - - - +
312A CYS* 3.4 3.0 - - - -
317A GLN* 3.6 46.1 - - + +
319A VAL 3.2 4.5 - - - -
320A GLU* 3.9 9.9 - - + +
372A ILE* 3.2 5.5 - - - +
373A LEU* 2.8 73.1 + - + +
375A VAL* 5.3 5.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A THR* 5.6 0.2 - - + -
310A LYS* 1.3 72.9 - - - +
312A CYS* 1.3 52.2 - - - +
317A GLN 3.3 2.1 - - - -
318A VAL* 2.7 32.8 + - + -
319A VAL* 2.9 34.3 + - + +
344A P1L 3.9 29.4 - - + -
346A TYR* 3.8 26.7 - - + -
347A MET* 3.9 22.4 - - + -
370A PHE* 4.3 10.8 - - + -
371A THR 3.7 4.0 - - - -
372A ILE* 4.0 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A PHE* 4.5 0.9 - - - -
252A PRO* 3.9 26.7 - - + -
310A LYS* 3.4 17.7 - - - -
311A VAL* 1.3 74.6 - - - +
313A SER* 1.3 59.9 + - - +
314A PHE 4.6 4.3 - - - +
316A LYS 3.4 11.9 - - - +
317A GLN* 3.6 13.5 - - - +
318A VAL* 4.5 0.7 - - - -
369A ASN 3.7 1.0 - - - +
370A PHE* 3.6 6.1 - - - -
371A THR* 2.5 63.0 + - - +
372A ILE 4.4 0.2 - - - -
373A LEU* 4.0 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A CYS* 1.3 71.4 - - - +
314A PHE* 1.3 74.1 + - - +
316A LYS* 2.7 26.1 + - - +
318A VAL* 3.5 12.9 - - - +
346A TYR* 4.1 3.8 - - - -
369A ASN 3.3 4.5 - - - -
370A PHE* 4.8 1.3 - - - +
58B ARG* 3.8 3.5 + - - -
64B ASP* 2.6 38.5 + - - -
68B LEU* 3.8 20.9 - - - -
----------------------------------------------------------
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