Contacts of the strand formed by residues 200 - 206 (chain B) in PDB entry 1QQJ
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 LEU 200 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B MET* 3.8 2.0 - - - -
199B GLU* 1.3 69.4 - - - +
201B GLU* 1.3 64.6 + - - +
231B MET 4.0 1.8 - - - -
299B LEU* 4.1 29.2 - - + -
300B SER 5.1 0.2 - - - +
301B VAL* 4.1 16.2 - - + -
315B CYS* 3.8 25.8 - - - -
317B SER* 3.9 18.2 - - - -
350B THR* 3.3 4.9 - - - +
351B ILE* 2.8 42.3 + - + +
360B GLY* 2.9 21.6 + - - +
392B ILE* 3.4 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ASP* 2.4 26.5 - - - +
199B GLU* 3.7 10.5 - - - +
200B LEU* 1.3 88.1 - - - +
202B MET* 1.3 71.9 + - - +
230B LEU* 3.8 2.6 - - - +
231B MET* 2.9 42.8 + - + +
233B ASP* 3.4 16.3 - - + +
347B ALA* 3.3 8.1 - - - +
348B SER* 3.6 8.7 - - - +
349B GLY 3.0 22.7 + - - +
350B THR* 3.7 4.8 + - - +
351B ILE* 3.7 5.2 - - - -
420B CA 2.6 23.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B GLU* 1.3 82.1 - - - +
203B ALA* 1.3 63.5 + - - +
228B MET* 3.7 20.6 - - + -
229B VAL 3.4 11.7 - - - +
230B LEU* 4.1 9.9 - - + -
231B MET* 4.3 1.3 - - - +
297B ILE* 3.8 26.0 - - + -
299B LEU* 3.9 20.6 - - + -
319B PHE* 3.8 24.9 - - + -
347B ALA* 3.5 1.0 - - - +
348B SER* 2.9 35.3 + - - -
351B ILE* 3.6 10.0 - - + +
405B PHE* 3.4 41.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B MET* 1.3 77.9 - - - +
204B PHE* 1.3 61.5 + - - +
205B PHE* 5.3 0.2 - - - -
228B MET* 3.2 8.2 - - - +
229B VAL* 2.9 40.2 + - + +
231B MET* 4.0 10.7 - - + +
345B LEU* 3.5 26.0 - - + -
346B LEU 3.4 11.7 - - - +
347B ALA* 3.7 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ALA* 1.3 75.3 - - - +
205B PHE* 1.3 65.7 + - - +
206B VAL* 4.6 3.8 - - + -
225B ILE* 3.7 35.0 - - + -
227B GLY 3.2 11.7 - - - +
228B MET* 4.3 3.1 - - + -
326B MET* 3.4 60.6 - - + -
329B GLN* 3.7 13.7 - - - -
330B LEU* 3.9 16.8 - - + -
344B ASP 3.6 0.2 - - - +
345B LEU* 3.5 6.5 - - - -
346B LEU* 2.9 73.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B MET* 3.6 28.0 - - + -
118B PRO* 3.9 17.0 - - + -
119B ALA* 4.0 9.6 - - + -
121B ILE* 3.9 15.9 - - + -
203B ALA 5.3 0.2 - - - -
204B PHE* 1.3 76.1 - - - +
206B VAL* 1.3 59.5 - - - +
225B ILE* 3.9 3.1 - - - -
226B PHE* 2.9 32.9 + - + +
227B GLY 2.9 10.5 + - - +
229B VAL* 3.8 26.5 - - + -
259B ILE* 4.1 11.7 - - + -
263B VAL* 3.8 27.1 - - + -
343B GLY* 3.4 27.1 - - - -
344B ASP 3.2 6.3 - - - -
345B LEU* 3.7 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B MET* 3.8 8.5 - - - +
204B PHE* 4.6 2.9 - - + -
205B PHE* 1.3 74.8 - - - +
207B GLY* 1.3 73.7 + - - +
208B PRO 3.8 11.7 - - - +
224B HIS* 3.4 12.6 - - + +
226B PHE* 4.5 1.3 - - - -
330B LEU* 4.3 16.8 - - + -
340B LEU* 4.2 18.4 - - + -
341B ARG 3.5 21.1 - - - +
342B PRO* 3.4 0.7 - - - +
343B GLY* 3.0 23.0 + - - -
344B ASP* 2.9 18.4 + - + +
346B LEU* 3.8 29.2 - - + -
----------------------------------------------------------
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