Contacts of the helix formed by residues 312 - 325 (chain B) 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 ASN 312 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ARG* 4.7 3.1 - - - +
137A GLN* 4.6 1.1 - - - -
307B ALA* 2.9 12.3 + - - +
310B ALA* 4.2 11.2 - - + +
311B GLN* 1.3 75.7 - - - +
313B PRO* 1.3 66.4 - - - +
314B LEU* 2.9 23.8 + - - +
315B GLN* 3.0 46.5 + - - +
316B ALA* 3.2 21.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ARG* 5.4 1.1 - - - +
134A TYR* 3.3 46.0 - - + -
137A GLN* 3.6 24.9 - - + +
311B GLN 3.4 9.8 - - - +
312B ASN* 1.3 85.1 - - - +
314B LEU* 1.3 72.2 + - + +
316B ALA* 3.8 6.1 - - + -
317B GLN* 2.9 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A TYR* 4.7 15.7 - - + +
312B ASN* 2.9 10.4 + - - +
313B PRO* 1.3 90.5 - - + +
315B GLN* 1.3 63.7 + - + +
317B GLN* 3.9 3.3 - - - +
318B ARG* 3.0 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ALA* 3.7 21.7 - - + +
310B ALA* 4.8 4.9 - - - +
312B ASN* 3.0 40.6 + - - +
314B LEU* 1.3 73.9 - - + +
316B ALA* 1.3 66.1 + - - +
318B ARG* 3.3 8.7 + - - +
319B ILE* 3.1 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PHE* 3.4 32.3 - - + +
137A GLN* 4.4 1.1 - - - +
304B LEU* 3.8 15.7 - - + -
307B ALA* 3.7 10.0 - - + +
308B GLN* 4.9 1.3 - - + -
312B ASN 3.2 18.6 + - - +
313B PRO* 3.8 6.1 - - + +
314B LEU 3.3 0.2 - - - -
315B GLN* 1.3 76.4 - - - +
317B GLN* 1.3 58.7 + - + +
319B ILE* 3.3 3.3 + - - +
320B VAL* 2.9 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A TYR* 4.4 18.3 - - + +
135A PRO* 3.0 37.4 + - - +
136A PHE* 4.7 1.8 - - - +
249B THR* 3.9 27.2 + - - +
313B PRO* 2.9 22.7 + - + +
314B LEU* 4.0 3.8 - - + +
316B ALA* 1.3 75.0 - - + +
318B ARG* 1.3 59.8 + - - +
320B VAL* 4.3 7.6 - - - +
321B GLN* 2.8 58.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B LEU 3.0 20.7 + - - +
315B GLN* 3.6 8.3 - - - +
317B GLN* 1.3 76.3 - - - +
319B ILE* 1.3 64.7 + - + +
321B GLN* 3.8 10.6 - - - +
322B ASP* 3.0 42.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B LEU* 3.9 17.5 - - + +
300B ASP* 3.6 32.9 + - + +
303B ALA* 3.5 40.4 - - + +
304B LEU* 3.7 11.0 - - + +
307B ALA* 4.5 3.1 - - + -
315B GLN* 3.1 25.1 + - + +
316B ALA* 3.5 6.5 - - - +
318B ARG* 1.3 78.1 - - + +
320B VAL* 1.3 63.2 + - - +
322B ASP* 3.3 17.6 + - - +
323B ALA* 3.3 9.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PHE* 3.5 59.9 - - + -
249B THR* 4.5 11.7 - - + +
252B PHE* 3.8 12.7 - - + -
299B LEU* 4.0 12.8 - - + -
304B LEU* 4.0 7.9 - - + -
316B ALA 2.9 21.2 + - - +
317B GLN* 3.7 10.5 - - - +
319B ILE* 1.3 75.5 - - - +
321B GLN* 1.3 61.8 + - + +
323B ALA* 3.1 4.2 + - - +
324B LEU* 2.9 31.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B THR* 6.2 0.4 - - - +
317B GLN* 2.8 45.9 + - - +
318B ARG* 3.8 10.5 - - - +
320B VAL* 1.3 75.9 - - + +
322B ASP* 1.3 64.9 + - - +
324B LEU* 4.5 3.8 - - - +
325B LEU* 2.9 52.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B LYS* 5.7 0.7 - - - +
318B ARG* 3.0 32.2 + - - +
319B ILE* 3.5 12.3 - - - +
320B VAL 3.2 0.4 - - - -
321B GLN* 1.3 78.7 - - - +
323B ALA* 1.3 60.6 + - - +
325B LEU 4.7 0.3 - - - -
326B SER* 4.1 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B PHE* 4.0 3.8 - - + -
295B ALA* 3.4 32.0 - - - +
298B LYS* 4.3 8.9 - - - +
299B LEU* 3.7 33.9 - - + +
319B ILE 3.3 1.9 + - - +
320B VAL 3.1 7.2 + - - +
322B ASP* 1.3 78.9 - - - +
324B LEU* 1.3 57.3 + - - +
326B SER* 2.6 29.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B MSE 3.8 44.0 - - + +
249B THR* 3.8 23.3 - - - +
252B PHE* 4.0 22.0 - - + -
288B PHE* 5.1 1.1 - - + -
291B HIS* 2.8 37.7 + - + +
292B ILE* 3.8 28.9 - - + -
295B ALA* 4.1 5.4 - - + -
320B VAL* 2.9 23.3 + - + +
321B GLN* 4.4 3.1 - - - +
323B ALA* 1.3 74.9 - - - +
325B LEU* 1.3 61.6 + - + +
326B SER 3.1 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B MSE 5.0 15.5 - - + -
321B GLN* 2.9 42.6 + - + +
322B ASP* 4.7 1.8 - - - +
324B LEU* 1.3 79.4 - - + +
326B SER* 1.4 65.8 + - - +
327B SER* 3.7 0.9 + - - -
----------------------------------------------------------
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