Contacts of the strand formed by residues 281 - 287 (chain B) in PDB entry 4TR8
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 GLY 281 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B SER* 3.6 14.9 - - - -
276B ASN* 5.2 2.5 + - - +
279B TYR* 3.2 4.4 + - - +
280B ARG* 1.3 77.2 - - - +
282B ILE* 1.3 66.5 + - - +
295B ALA* 4.1 5.5 - - - +
296B ASN 5.4 0.7 + - - +
320B PHE 3.4 9.0 - - - -
365B MET* 3.8 22.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B PHE* 3.5 34.1 - - + -
271B THR* 3.9 16.4 - - - +
272B ALA* 4.4 7.6 - - - -
280B ARG 4.0 0.2 + - - -
281B GLY* 1.3 79.5 - - - +
283B ARG* 1.3 59.7 + - - +
284B LEU* 3.8 18.9 + - + +
293B ILE* 3.9 8.5 - - + -
294B GLN 3.5 6.3 - - - +
295B ALA* 4.0 13.5 - - + -
319B GLY* 3.4 3.6 - - - -
320B PHE 2.9 40.0 + - - +
322B VAL* 3.9 31.4 - - + -
325B LEU* 3.9 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ILE* 1.3 73.7 - - - +
284B LEU* 1.3 65.8 + - - +
285B GLN* 3.6 32.1 + - - +
292B LYS 3.7 1.0 - - - +
293B ILE* 3.5 5.5 - - - +
294B GLN* 2.8 81.8 + - - +
302B GLU* 5.3 1.0 + - - -
304B GLU* 4.7 5.9 + - - -
317B GLU* 3.6 35.4 + - + -
318B ILE 3.8 5.8 - - - +
319B GLY* 4.5 2.0 - - - -
367B LEU* 5.2 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B PHE* 4.4 13.9 - - + -
282B ILE* 3.8 32.8 - - + +
283B ARG* 1.3 78.6 - - - +
285B GLN* 1.3 62.7 + - - +
286B LEU* 3.9 1.3 - - + -
291B LEU* 3.9 33.2 - - + -
292B LYS 3.4 3.8 - - - +
293B ILE* 4.9 2.2 - - + -
316B LEU 3.5 1.0 - - - +
317B GLU* 3.3 5.7 - - - +
318B ILE* 2.8 52.6 + - + +
320B PHE* 4.1 29.6 - - + -
325B LEU* 4.4 3.1 - - + -
339B PHE* 5.8 6.5 - - + -
341B LEU* 5.8 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B ARG* 3.6 32.3 + - - +
284B LEU* 1.3 75.7 - - - +
286B LEU* 1.3 60.8 - - - +
287B SER* 4.1 1.6 + - - -
290B LEU 3.8 1.0 - - - +
291B LEU* 3.7 2.4 - - - -
292B LYS* 2.8 70.6 + - + +
294B GLN* 6.0 0.4 - - - +
304B GLU* 5.2 2.6 + - - -
316B LEU 3.5 3.4 - - - +
317B GLU* 2.9 34.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B LYS* 4.5 4.5 - - + -
257B VAL* 3.6 32.1 - - + -
284B LEU* 3.9 1.1 - - + -
285B GLN* 1.3 73.0 - - - +
287B SER* 1.3 61.9 + - - +
290B LEU 3.6 13.7 - - - +
291B LEU* 4.1 20.6 - - + -
309B VAL* 4.2 11.0 - - + -
311B TYR* 3.7 39.5 - - + +
314B GLY 4.7 0.2 - - - -
315B ASN* 3.3 7.8 - - - +
316B LEU* 2.8 51.2 + - + +
318B ILE* 6.3 0.9 - - + -
341B LEU* 4.2 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B GLN 5.0 1.4 + - - -
286B LEU* 1.3 75.5 - - - +
288B ASN* 1.3 69.2 + - - +
289B GLY 3.1 0.9 + - - -
290B LEU* 3.0 41.4 + - - +
292B LYS* 5.6 2.1 - - - +
311B TYR* 3.3 17.6 - - - -
314B GLY 4.6 1.3 - - - -
315B ASN* 3.4 22.7 - - - -
----------------------------------------------------------
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