Contacts of the helix formed by residues 300 - 311 (chain A) in PDB entry 3KTC
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 ASP 300 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LYS 3.3 4.6 + - - +
299A LEU* 1.3 73.6 - - - +
301A ILE* 1.3 59.0 + - - +
302A PRO* 3.4 11.9 - - - +
303A ALA* 3.2 31.4 + - + +
304A LEU* 2.9 26.9 + - - +
319A ILE* 3.7 12.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A TYR* 4.0 18.6 - - + -
259A LYS* 3.6 35.9 - - + -
260A ILE* 4.4 3.6 - - + -
296A LEU 4.8 2.2 - - - +
299A LEU* 3.1 32.2 + - + +
300A ASP* 1.3 71.4 - - - +
302A PRO* 1.3 67.8 - - + +
304A LEU* 3.1 5.5 + - - +
305A GLN* 2.8 54.1 + - + +
338A UNL 3.7 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ASP* 3.4 10.3 - - - +
301A ILE* 1.3 92.5 - - + +
303A ALA* 1.3 55.6 + - - +
305A GLN* 3.4 7.5 + - + +
306A ALA* 3.0 28.2 + - - +
338A UNL 3.8 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ASP* 3.2 34.7 + - + +
302A PRO* 1.3 73.8 - - - +
304A LEU* 1.3 66.2 + - - +
306A ALA* 3.3 7.7 + - - +
307A ALA* 3.0 18.2 + - - +
319A ILE* 3.5 24.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A TYR* 3.7 34.8 - - + +
299A LEU* 4.1 12.6 - - + -
300A ASP 2.9 14.5 + - - +
301A ILE* 3.5 6.5 - - - +
303A ALA* 1.3 77.4 - - - +
305A GLN* 1.3 57.6 + - - +
307A ALA* 3.1 5.1 + - - +
308A GLN* 2.9 47.1 + - - +
316A ALA* 3.7 36.8 - - + +
319A ILE* 3.7 14.9 - - + +
320A VAL* 4.1 9.9 - - + -
136B PHE* 3.8 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A TYR* 3.1 26.7 + - - +
260A ILE* 4.0 18.0 - - - +
301A ILE* 2.8 39.3 + - - +
302A PRO* 3.9 6.2 - - + +
304A LEU* 1.3 72.7 - - - +
306A ALA* 1.3 58.1 + - - +
308A GLN* 3.3 12.7 + - - +
309A GLU* 2.9 27.5 + - - +
338A UNL 4.0 15.3 + - - +
344A EDO 4.9 4.6 + - - -
139B SER* 6.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A PRO 3.0 17.1 + - - +
303A ALA* 3.6 7.9 - - - +
304A LEU 3.2 0.2 - - - -
305A GLN* 1.3 76.0 - - - +
307A ALA* 1.3 61.7 + - - +
309A GLU* 3.3 8.5 + - - +
310A ALA* 3.2 21.1 + - - +
315A GLN* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ALA 3.0 12.1 + - - +
304A LEU 3.4 8.7 - - - +
306A ALA* 1.3 76.0 - - - +
308A GLN* 1.3 56.5 - - - +
310A ALA* 3.2 3.6 + - - +
311A GLN 2.9 21.8 + - - -
312A ASN 2.9 13.7 + - - +
315A GLN* 3.7 26.9 - - + +
316A ALA* 3.6 32.5 - - - +
319A ILE* 4.4 2.0 - - + -
137B GLN 4.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A GLU* 5.3 0.8 + - - -
256A TYR* 3.9 19.6 + - - -
304A LEU* 2.9 37.2 + - + +
305A GLN* 3.6 13.6 - - - +
306A ALA 3.2 0.4 - - - -
307A ALA* 1.3 74.8 - - - +
309A GLU* 1.3 63.4 + - - +
311A GLN* 3.0 13.0 + - - +
316A ALA* 4.8 0.4 - - + -
136B PHE* 2.9 41.1 + - - +
137B GLN 3.5 10.0 - - - +
138B VAL 3.3 17.4 + - - -
139B SER* 3.6 26.2 + - - +
344B EDO 2.8 21.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A GLN 2.9 13.9 + - - +
306A ALA* 3.3 11.4 + - - +
308A GLN* 1.3 75.3 - - - +
310A ALA* 1.3 60.5 + - - +
311A GLN* 3.3 4.3 + - - +
96B PRO* 3.6 23.7 - - - +
101B ARG* 5.3 6.2 + - - -
142B ASN* 4.6 10.2 + - - -
344B EDO 3.6 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ALA 3.2 11.2 + - - +
307A ALA* 3.2 9.7 + - - +
309A GLU* 1.3 75.0 - - - +
311A GLN* 1.3 60.5 + - - +
312A ASN* 3.3 12.5 + - + +
315A GLN* 4.8 4.3 - - - +
90B ARG* 2.9 23.6 + - - -
96B PRO* 3.8 11.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ALA 2.9 5.2 + - - -
308A GLN 3.0 18.0 + - - +
309A GLU 4.0 1.7 + - - +
310A ALA* 1.3 80.4 - - - +
312A ASN* 1.3 58.5 + - - +
313A PRO* 3.2 2.2 - - - +
90B ARG* 3.0 22.9 + - - +
94B THR* 2.8 29.0 + - - +
95B ASN 4.5 0.2 + - - -
96B PRO* 3.7 22.1 - - + +
131B GLY 4.3 8.8 - - - +
137B GLN* 3.0 36.5 + - + +
138B VAL* 4.2 13.3 - - + +
143B LEU* 4.3 4.7 - - - +
146B LEU* 4.9 1.6 - - - +
173B ARG* 4.8 5.2 + - - -
344B EDO 3.4 27.6 + - - -
----------------------------------------------------------
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