Contacts of the strand formed by residues 318 - 322 (chain B) in PDB entry 1Q6X
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 318 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LEU* 3.5 31.8 + - + +
169B PHE* 3.5 28.5 - - + -
277B ILE 5.6 0.2 - - - +
278B CYS* 3.6 8.8 - - + +
279B LEU* 3.0 25.0 + - - +
316B LYS* 3.4 6.9 - - - +
317B SER* 1.3 79.5 - - - +
319B GLN* 1.3 64.1 - - - +
320B PHE* 4.0 22.0 - - + -
330B VAL* 4.0 10.1 - - + -
331B VAL 4.0 0.4 - - - -
332B CYS* 3.7 15.7 - - + -
337B PHE* 3.9 8.5 - - + -
342B LEU* 3.5 31.2 - - + -
345B CYS* 5.1 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B LEU* 3.6 22.6 - - + +
281B CYS* 4.2 6.7 - - - -
312B ARG* 3.3 20.0 - - - +
313B TRP 2.6 49.3 + - - +
314B TYR* 3.7 22.0 - - - -
316B LYS* 4.3 8.4 - - + +
318B LEU* 1.3 78.2 - - - +
320B PHE* 1.3 62.9 + - - +
321B VAL* 3.6 1.7 + - - +
330B VAL* 3.4 4.8 - - - +
331B VAL* 3.0 59.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PHE* 4.8 4.0 - + - -
130B LEU* 3.8 38.6 - - + -
134B VAL* 4.1 11.2 - - + -
169B PHE* 4.9 2.0 - + - -
278B CYS* 3.8 25.1 - - + -
279B LEU 2.8 18.1 + - - +
280B VAL* 3.4 8.4 - - + +
281B CYS* 2.7 33.3 + - - +
318B LEU* 4.2 28.3 - - + -
319B GLN* 1.3 72.9 - - - +
321B VAL* 1.3 55.5 + - - +
322B VAL* 4.0 1.2 + - + -
329B GLY 3.5 3.4 - - - +
330B VAL* 3.2 34.1 - - + -
345B CYS* 5.6 1.6 - - - -
346B THR* 5.1 5.2 - - + -
349B LEU* 3.8 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PHE* 5.6 0.3 - - - -
281B CYS* 3.5 11.0 - - + +
283B ASP* 3.6 29.2 - - + +
298B GLN* 4.6 2.9 - - - +
299B LEU* 3.7 36.1 - - + -
312B ARG* 3.9 26.5 - - - +
319B GLN 4.0 7.2 - - - +
320B PHE* 1.3 75.8 - - - +
322B VAL* 1.3 66.2 + - - +
323B GLY 4.3 1.6 - - - +
327B THR 4.1 11.4 - - - +
328B CYS* 3.0 27.0 - - - +
329B GLY 2.8 12.8 + - - +
331B VAL* 4.6 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B PHE* 4.1 4.3 - - + -
123B GLN* 2.9 50.8 + - + +
126B PHE* 3.9 27.4 - - + -
127B ALA* 4.2 20.4 - - + -
130B LEU* 4.5 14.1 - - + -
280B VAL* 4.6 12.1 - - + -
281B CYS 2.9 12.0 + - - +
282B LEU* 3.5 15.7 - - + -
320B PHE 4.8 0.9 - - - +
321B VAL* 1.3 78.6 - - - +
323B GLY* 1.3 59.3 + - - +
328B CYS* 3.8 9.4 - - - -
----------------------------------------------------------
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