Contacts of the strand formed by residues 292 - 299 (chain B) in PDB entry 5HKE
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 292 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ASN* 6.1 0.4 - - - +
288B THR* 3.8 3.8 - - - -
289B THR* 3.1 38.6 + - + +
290B TYR 3.4 0.4 - - - -
291B GLU* 1.3 76.7 - - - +
293B ARG* 1.3 65.8 + - - +
294B GLN* 3.2 26.9 + - - +
296B VAL* 4.7 11.3 - - - +
315B GLU* 4.1 16.3 + - - +
317B LYS 3.2 19.6 + - - +
318B GLN* 3.5 2.3 - - - +
319B ILE* 3.0 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A PHE* 4.1 26.4 + - + +
250A HIS* 6.1 4.9 - - + +
253A GLY* 5.8 4.2 - - - -
256A GLU* 5.1 9.1 + - - -
275A SER* 5.9 1.0 + - - -
288A THR* 3.4 23.2 + - - +
289A THR 5.4 1.2 + - - -
293A ARG* 2.9 103.7 + - - +
294A GLN* 4.8 1.1 - - - -
295A ILE* 3.8 22.2 - - + -
250B HIS* 6.2 1.2 - - - -
288B THR* 3.6 1.4 - - - +
289B THR 4.9 0.7 - - - -
290B TYR 6.1 0.4 - - - +
292B ASN* 1.3 72.4 - - - +
294B GLN* 1.3 63.8 + - - +
295B ILE 3.3 0.5 + - - -
318B GLN* 2.8 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A GLN* 3.5 49.9 + - + +
319A ILE* 3.0 36.1 + - - +
320A ILE 4.2 0.6 - - - -
321A ASN* 3.8 27.4 + - + +
287B TYR 3.9 4.5 - - - +
288B THR* 4.3 1.1 - - - +
292B ASN* 3.2 30.4 + - - +
293B ARG* 1.3 79.0 - - - +
295B ILE* 1.3 71.9 + - - +
296B VAL* 3.5 5.0 + - - +
318B GLN* 4.4 0.6 + - - -
319B ILE* 3.7 19.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ARG* 3.7 18.0 - - - +
318A GLN* 3.7 37.0 + - + +
319A ILE 4.6 1.6 + - - +
320A ILE* 3.4 16.4 - - + -
321A ASN* 2.9 31.2 + - - +
245B ILE* 4.6 7.2 - - + +
249B PHE* 3.8 18.8 - - + -
286B TYR* 3.7 37.9 - - + -
287B TYR 3.4 8.7 - - - +
288B THR* 3.7 17.7 - - + -
293B ARG 3.3 0.4 + - - -
294B GLN* 1.3 76.1 - - - +
296B VAL* 1.3 59.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ASN* 3.3 27.1 - - + +
323A LEU* 3.8 26.5 - - + -
285B LEU 3.7 1.0 - - - +
286B TYR* 3.1 4.7 - - - -
287B TYR* 2.8 76.4 + - + +
292B ASN* 4.7 10.8 - - - +
294B GLN* 3.9 9.6 - - + +
295B ILE* 1.3 76.8 - - - +
297B ALA* 1.3 63.1 + - - +
312B TYR* 5.0 1.1 - - + -
315B GLU* 6.3 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ILE* 3.7 21.7 - - + +
321A ASN 2.9 7.9 + - - +
322A LYS* 3.8 12.2 - - + +
323A LEU* 2.9 29.8 + - - +
284B THR* 4.4 5.4 - - + -
285B LEU 3.2 5.6 - - - +
286B TYR* 3.7 22.2 - - + -
296B VAL* 1.3 75.0 - - - +
298B VAL* 1.3 62.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LEU* 4.5 24.9 - - + +
28B VAL* 3.9 25.8 - - + -
30B ILE* 4.4 10.1 - - + -
52B ILE* 3.7 17.1 - - + +
284B THR* 4.2 0.9 - - - +
285B LEU* 2.8 54.6 + - + +
287B TYR* 4.9 4.5 - - + -
297B ALA* 1.3 75.8 - - - +
299B THR* 1.3 72.7 + - - +
312B TYR* 6.2 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LEU 5.9 1.0 - - - -
30B ILE* 4.1 7.6 - - - +
52B ILE* 4.1 3.1 - - - -
282B ASN 3.8 8.3 - - - +
283B LYS* 3.5 13.7 - - + +
284B THR* 3.0 23.5 + - - +
298B VAL* 1.3 84.3 - - - +
300B LEU* 1.3 75.5 + - - +
----------------------------------------------------------
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