Contacts of the helix formed by residues 750 - 755 (chain B) in PDB entry 1QCO
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 PHE 750 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A THR* 3.6 32.1 - - + -
127A PHE* 4.4 16.4 - + - -
156A PRO 5.4 0.2 - - - -
157A VAL* 6.1 0.2 - - - -
158A GLY* 3.7 27.6 - - - +
159A TYR* 4.0 10.8 - - - -
160A HIS* 3.6 35.1 + + - -
332A HIS* 4.5 11.9 - + - -
333A HIS* 3.8 21.1 - + - -
743B GLU* 2.9 21.4 + - + +
748B GLY 3.5 3.6 + - - +
749B PRO* 1.3 74.8 - - - +
751B LEU* 1.3 92.7 + - + +
752B GLY 3.1 1.0 - - - +
753B LYS* 3.2 4.2 + - - +
754B SER* 3.1 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 751 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A HIS* 3.3 49.4 - - + +
333A HIS* 3.7 23.8 - - - +
335A VAL* 3.7 13.9 - - + -
336A ASN* 2.8 42.2 + - + +
678B GLY* 6.0 1.3 - - - -
679B GLN 6.2 0.7 - - - +
736B ALA* 5.0 0.7 - - - +
739B ILE* 4.1 15.0 - - + +
743B GLU* 2.9 13.6 + - - +
750B PHE* 1.3 94.9 - - + +
752B GLY* 1.3 60.8 + - - +
753B LYS 3.0 7.0 + - - -
754B SER* 3.6 6.3 - - - +
755B PHE* 3.6 7.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 752 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735B SER* 3.3 7.8 - - - -
736B ALA* 2.9 45.1 + - - +
739B ILE* 4.0 6.7 - - - +
740B GLN* 4.2 9.9 - - - +
743B GLU* 2.9 16.7 + - - -
751B LEU* 1.3 76.5 - - - +
753B LYS* 1.3 63.7 + - - +
755B PHE* 3.4 3.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 753 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A HIS* 5.5 2.5 - - - +
659B TYR* 3.8 15.0 - - + +
699B GLU* 2.9 29.3 + - - -
733B ASP* 3.5 17.9 - - - +
734B TRP 3.7 5.6 - - - +
735B SER* 2.7 30.5 + - - +
737B ARG* 4.0 4.2 - - - +
740B GLN* 3.5 18.8 - - - +
749B PRO* 3.7 23.3 - - + -
750B PHE 3.2 5.3 + - - +
751B LEU 3.0 0.4 - - - -
752B GLY* 1.3 83.2 - - - +
754B SER* 1.3 62.0 + - - +
755B PHE* 3.2 6.1 + - - -
756B GLY 3.5 18.4 + - - +
757B THR* 3.9 7.8 + - - -
1011B AAE 3.2 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 754 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A HIS* 4.0 10.2 - - - -
333A HIS* 5.3 0.3 - - - -
336A ASN* 3.2 17.1 + - - -
338A CYS* 3.7 16.7 - - - +
662B ARG* 3.6 28.7 - - - +
665B SER* 2.7 29.1 + - - -
750B PHE 3.1 15.8 + - - -
751B LEU* 3.6 10.4 + - - +
753B LYS* 1.3 73.1 - - - +
755B PHE* 1.3 55.1 + - - +
756B GLY 3.1 6.5 - - - -
757B THR* 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 755 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A PHE* 3.2 24.5 - - - -
213A GLY* 5.8 0.7 + - - -
336A ASN* 3.2 36.0 - - - +
337A GLY 5.1 2.3 - - - +
338A CYS 4.5 4.9 - - - +
673B ILE* 3.9 19.7 - - + +
674B ARG 4.1 4.7 - - - +
676B PRO* 4.0 20.9 - - + -
696B LEU* 3.6 28.7 - - + -
734B TRP* 3.6 40.8 - - + -
735B SER 3.8 1.1 - - - -
736B ALA* 3.6 11.4 - - + -
751B LEU 3.6 14.1 - - - -
752B GLY 3.4 22.4 - - - -
753B LYS 4.2 1.3 - - - -
754B SER* 1.3 76.9 - - - +
756B GLY* 1.3 56.0 + - - +
----------------------------------------------------------
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