Contacts of the helix formed by residues 73 - 79 (chain A) in PDB entry 2VQQ
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 GLU 73 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLN* 3.4 31.4 + - - +
71A HIS 3.9 0.8 + - - -
72A SER* 1.3 72.4 - - - +
74A ALA* 1.3 58.1 + - - +
76A THR* 3.2 2.3 + - - -
77A LEU* 2.8 57.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A SER* 3.3 7.2 + - - +
73A GLU* 1.3 77.8 - - - +
75A HIS* 1.3 64.3 + - - +
77A LEU* 3.8 7.5 - - - +
78A LEU* 2.9 27.5 + - - +
224B GLY 5.9 2.5 - - - +
225B ASN* 5.3 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A HIS* 3.7 25.3 + - + -
72A SER* 3.1 22.8 + - - +
74A ALA* 1.3 78.4 - - - +
76A THR* 1.3 61.2 + - - +
78A LEU* 4.7 1.8 - - - -
79A TYR* 3.1 53.8 + + - +
162A GLU 3.9 9.2 - - - +
163A SER* 3.9 17.8 + - - +
164A THR 4.2 4.3 - - - -
165A PRO* 3.7 26.4 - - + +
170A TYR 2.8 28.5 + - - -
171A PHE* 3.7 16.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU* 3.6 30.0 - - + +
67A LEU* 3.6 37.0 - - + +
68A GLN* 3.4 17.1 - - + +
71A HIS* 3.8 13.0 - - - +
72A SER 2.8 19.0 + - - -
73A GLU 3.6 3.4 - - - -
75A HIS* 1.3 75.2 - - - +
77A LEU* 1.3 57.0 + - - +
80A GLY* 2.8 34.7 + - - -
171A PHE* 4.2 8.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU* 3.9 25.4 - - + -
68A GLN* 5.6 2.5 - - - +
73A GLU* 2.8 48.4 + - + +
74A ALA* 3.8 6.3 - - - +
76A THR* 1.3 74.5 - - - +
78A LEU* 1.3 62.0 + - - +
81A THR* 2.7 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ALA 2.9 17.8 + - - +
75A HIS* 3.8 4.3 - - - +
77A LEU* 1.3 79.1 - - - +
79A TYR* 1.3 89.9 + - + +
81A THR* 4.2 2.4 - - - +
226B PHE* 6.4 0.7 - - - -
227B PHE* 4.4 20.6 - - + +
298B PRO* 4.8 13.0 - - + +
1409B TFG 3.3 54.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A HIS* 3.1 43.9 + + - +
78A LEU* 1.3 95.3 - - + +
80A GLY* 1.3 62.2 + - - +
81A THR 3.5 1.0 - - - +
124A ALA* 3.6 21.8 - - + +
125A GLY* 4.6 1.2 + - - -
165A PRO* 3.6 20.4 - - + +
170A TYR* 3.6 30.3 - + + -
171A PHE* 3.8 18.6 - - + -
227B PHE* 3.7 28.2 - - - -
1409B TFG 3.5 57.4 - + - -
----------------------------------------------------------
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