Contacts of the helix formed by residues 296 - 320 (chain B) in PDB entry 1KB6
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 THR 296 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B LYS* 4.7 1.1 - - - +
294B ILE 4.7 4.7 - - - +
295B LEU* 1.3 74.5 - - - +
297B ASP* 1.3 59.2 + - - +
298B GLU* 3.5 10.3 + - - +
299B GLU* 2.8 51.5 + - - +
300B VAL* 2.9 28.4 + - - +
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Residues in contact with ASP 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B LYS* 4.2 21.0 + - - +
295B LEU 4.1 0.8 + - - -
296B THR* 1.3 74.1 - - - +
298B GLU* 1.3 61.3 + - - +
300B VAL* 3.9 11.1 - - - +
301B GLN* 3.3 21.8 + - - +
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Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A THR* 5.7 6.0 - - - +
296B THR* 3.0 7.9 + - - +
297B ASP* 1.3 77.0 - - - +
299B GLU* 1.3 79.3 + - - +
301B GLN* 3.1 14.4 + - - +
302B ARG* 3.1 19.4 + - + +
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Residues in contact with GLU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A THR* 4.9 12.9 + - + +
61A PRO* 5.9 4.3 - - - +
292B GLU 5.6 1.7 - - - +
294B ILE 4.6 1.0 - - - +
295B LEU* 3.9 28.5 - - + +
296B THR* 2.8 52.9 + - - +
298B GLU* 1.3 89.5 - - - +
300B VAL* 1.3 63.5 + - - +
301B GLN 3.2 0.2 + - - -
302B ARG* 3.2 9.3 + - - +
303B LYS* 3.1 19.9 + - - +
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Residues in contact with VAL 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B LYS* 5.0 4.9 - - - +
295B LEU* 3.9 28.3 - - + +
296B THR 2.9 17.8 + - - +
297B ASP* 3.9 12.3 - - - +
299B GLU* 1.3 75.8 - - - +
301B GLN* 1.3 69.6 + - - +
303B LYS* 3.1 16.6 + - + +
304B ARG* 3.2 13.9 + - + +
414C G 4.1 17.7 - - - +
415C G 3.6 23.3 - - - +
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Residues in contact with GLN 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ASP 3.3 11.8 + - - +
298B GLU* 3.1 10.8 + - - +
300B VAL* 1.3 81.1 + - - +
302B ARG* 1.3 56.3 + - - +
303B LYS 2.6 16.1 + - - -
304B ARG* 2.9 24.1 + - - +
305B GLU* 3.0 15.0 + - + +
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Residues in contact with ARG 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B GLU* 3.1 15.1 + - + +
299B GLU* 3.2 12.1 + - - +
301B GLN* 1.3 77.3 - - - +
303B LYS* 1.3 56.0 + - - +
305B GLU* 3.9 6.4 - - - +
306B MET* 2.8 31.7 + - - +
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Residues in contact with LYS 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 5.6 5.8 - - + -
299B GLU 3.1 9.9 + - - +
300B VAL* 3.1 14.1 + - + +
301B GLN 2.6 5.1 + - - -
302B ARG* 1.3 70.9 - - - +
304B ARG* 1.3 56.4 + - - +
305B GLU 2.9 1.3 - - - -
306B MET* 2.9 6.9 + - - +
307B ILE* 2.7 43.4 + - + +
426D A 6.6 0.2 - - - -
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Residues in contact with ARG 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B VAL* 3.2 8.3 + - + +
301B GLN* 2.9 22.1 + - - +
303B LYS* 1.3 74.7 - - - +
305B GLU* 1.3 56.8 + - - +
307B ILE* 3.3 31.0 - - + +
308B LEU* 3.3 18.3 - - - +
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Residues in contact with GLU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B GLN* 3.0 16.5 + - + +
302B ARG* 3.9 7.6 - - - +
303B LYS 2.9 0.2 - - - -
304B ARG* 1.3 74.4 - - - +
306B MET* 1.3 56.1 + - - +
307B ILE 2.9 4.3 - - - -
308B LEU* 2.7 30.2 + - - +
309B LYS* 3.0 14.0 + - - +
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Residues in contact with MET 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ARG 2.8 25.0 + - - +
303B LYS* 3.6 6.3 - - - +
305B GLU* 1.3 71.3 - - - +
307B ILE* 1.3 60.7 + - - +
309B LYS* 4.1 7.4 - - - +
310B ARG* 3.6 22.0 + - - +
426D A 6.3 0.2 - - - -
427D T 5.8 3.8 - - - +
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Residues in contact with ILE 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B LYS* 2.7 21.0 + - + +
304B ARG* 3.3 25.8 - - - +
306B MET* 1.3 80.6 - - - +
308B LEU* 1.3 67.5 + - + +
310B ARG* 3.8 3.0 + - - +
311B LYS* 3.1 29.3 + - + +
425D C 5.0 12.6 - - - +
426D A 4.1 39.9 + - - +
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Residues in contact with LEU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ARG 3.3 17.0 - - - +
305B GLU* 2.7 17.4 + - - +
307B ILE* 1.3 79.2 - - + +
309B LYS* 1.3 58.4 + - - +
311B LYS* 2.8 45.5 - - + +
312B GLU* 3.0 25.9 + - - +
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Residues in contact with LYS 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B GLU 3.0 13.0 + - - +
306B MET* 4.6 6.7 - - - +
308B LEU* 1.3 72.0 - - - +
310B ARG* 1.3 65.8 + - - +
311B LYS 3.0 1.6 - - - -
312B GLU* 3.2 14.1 + - - +
313B GLU* 3.0 36.1 + - - +
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Residues in contact with ARG 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B MET 3.6 17.4 + - - +
307B ILE* 4.1 3.1 - - - +
308B LEU 3.4 0.2 - - - -
309B LYS* 1.3 78.3 - - - +
311B LYS* 1.3 52.8 + - - +
313B GLU* 3.2 16.3 + - - +
314B GLU* 2.9 34.0 + - - +
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Residues in contact with LYS 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ILE* 3.1 18.9 + - + +
308B LEU* 2.8 41.0 - - + +
310B ARG* 1.3 79.7 - - - +
312B GLU* 1.3 63.0 + - + +
313B GLU 3.3 0.2 - - - -
314B GLU* 3.8 6.1 + - - +
315B ALA* 3.5 17.8 + - - +
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Residues in contact with GLU 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B LEU* 3.0 21.7 + - - +
309B LYS* 3.2 13.8 + - - +
311B LYS* 1.3 81.4 - - + +
313B GLU* 1.3 61.0 + - + +
314B GLU 3.4 0.7 - - - -
315B ALA* 3.5 9.8 - - + +
316B LEU* 3.2 24.8 + - - +
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Residues in contact with GLU 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B LYS* 3.0 29.9 + - - +
310B ARG* 3.2 17.3 + - - +
312B GLU* 1.3 79.3 - - + +
314B GLU* 1.3 59.2 + - - +
315B ALA 3.2 1.1 - - - -
316B LEU* 4.5 10.0 - - + +
317B LYS* 3.0 27.6 + - - +
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Residues in contact with GLU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B ARG 2.9 16.1 + - - +
311B LYS* 4.1 7.9 - - - +
313B GLU* 1.3 76.6 - - - +
315B ALA* 1.3 59.1 + - - +
317B LYS* 3.8 11.3 - - - +
318B ASP* 3.1 26.2 + - - +
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Residues in contact with ALA 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B LYS 3.5 13.8 + - - +
312B GLU* 3.5 14.1 - - + +
314B GLU* 1.3 77.4 - - - +
316B LEU* 1.3 60.6 + - - +
318B ASP* 2.9 28.2 + - - +
319B SER* 3.1 7.1 + - - -
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Residues in contact with LEU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B GLU 3.2 14.1 + - - +
313B GLU* 4.5 9.4 - - + +
315B ALA* 1.3 78.6 - - - +
317B LYS* 1.3 60.4 + - - +
319B SER* 2.7 26.7 + - - +
320B LEU* 3.2 34.5 - - + +
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Residues in contact with LYS 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B GLU 3.0 20.6 + - - +
314B GLU* 3.8 17.9 - - - +
315B ALA 3.2 0.4 - - - -
316B LEU* 1.3 78.9 - - - +
318B ASP* 1.3 64.7 + - - +
320B LEU* 4.0 10.8 + - - +
321B ARG* 4.3 5.2 + - - +
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Residues in contact with ASP 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B GLU 3.1 13.8 + - - +
315B ALA* 2.9 17.1 + - - +
317B LYS* 1.3 76.4 - - - +
319B SER* 1.3 63.5 + - - +
321B ARG* 2.9 27.0 + - - +
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Residues in contact with SER 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B ALA 3.1 5.3 + - - -
316B LEU* 2.7 33.0 + - - +
318B ASP* 1.3 76.6 - - - +
320B LEU* 1.3 68.3 + - - +
321B ARG* 2.9 9.0 + - - +
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Residues in contact with LEU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B LEU* 3.2 41.0 + - + +
317B LYS* 4.0 9.2 + - - +
318B ASP 3.1 1.6 + - - -
319B SER* 1.3 81.6 - - - +
321B ARG* 1.3 62.5 - - - +
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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
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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) + - + + + + + -
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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