Contacts of the helix formed by residues 70 - 81 (chain A) in PDB entry 1QAP
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 LYS 70 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PHE* 3.8 7.5 - - + -
69A GLY* 1.3 75.0 - - - +
71A ARG* 1.3 67.5 + - + +
73A VAL* 3.1 13.9 + - - +
74A GLU* 3.2 27.2 + - - +
89A TRP* 3.7 62.8 - - + +
91A VAL 4.5 3.4 - - - +
92A ASP* 3.0 29.9 + - - +
93A ASP* 2.9 21.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASN* 5.2 11.0 + - - +
22A ILE* 3.5 30.3 - - + +
23A PRO* 6.1 1.8 - - - +
69A GLY 3.4 0.6 - - - -
70A LYS* 1.3 80.0 - - + +
72A TRP* 1.3 69.5 + - + +
74A GLU* 3.7 35.7 + - - +
75A GLU* 3.2 40.5 + - - +
78A ILE* 3.9 13.5 - - - +
93A ASP* 4.1 5.7 + - - +
164A TYR* 5.9 1.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 3.7 19.7 - - + -
22A ILE* 3.7 39.4 - - + +
25A ALA* 5.5 3.8 - - + +
26A VAL* 4.0 8.2 - - + +
69A GLY* 3.6 24.9 - - - +
70A LYS 3.2 0.6 - - - -
71A ARG* 1.3 84.5 - - + +
73A VAL* 1.3 65.2 + - - +
75A GLU* 3.3 3.1 + - - +
76A VAL* 3.1 22.3 + - - +
93A ASP* 4.4 0.7 - - - -
123A PHE* 3.6 49.9 - + + -
127A LEU* 3.6 15.3 - - + -
161A ALA* 3.6 28.5 - - + +
164A TYR* 3.2 47.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLY 3.1 16.8 - - - +
70A LYS 3.1 6.3 + - - +
72A TRP* 1.3 73.5 - - + +
74A GLU* 1.3 69.3 + - - +
76A VAL* 2.7 31.4 + - + +
77A PHE* 3.5 16.4 + - + -
87A LEU* 3.9 11.4 - - + -
89A TRP* 3.4 28.3 - - + -
104A PHE* 4.3 19.5 - - + -
120A ALA* 4.6 12.3 - - + +
123A PHE* 5.9 0.4 - - + -
124A VAL* 3.5 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LYS* 3.2 29.4 + - - +
71A ARG* 3.8 31.9 + - - +
73A VAL* 1.3 79.1 - - - +
75A GLU* 1.3 62.7 + - - +
77A PHE* 3.6 2.6 + - - +
78A ILE* 3.1 31.7 + - + +
87A LEU* 4.0 16.6 - - + +
89A TRP* 3.7 27.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 3.9 12.8 - - + -
23A PRO* 3.2 28.0 - - + +
26A VAL* 3.8 19.3 - - + -
71A ARG* 3.2 33.9 + - - +
72A TRP 3.4 9.4 - - - +
73A VAL 3.0 0.8 - - - -
74A GLU* 1.3 78.2 - - - +
76A VAL* 1.3 57.2 + - - +
78A ILE* 3.1 18.3 + - - +
79A GLN* 2.7 53.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A VAL* 3.5 15.2 - - + +
30A LEU* 3.4 30.7 - - + +
72A TRP 3.1 10.0 + - - +
73A VAL* 2.7 36.5 + - - +
75A GLU* 1.3 72.2 - - - +
77A PHE* 1.3 83.8 + - + +
79A GLN* 3.5 3.3 + - - +
80A LEU* 3.2 26.9 + - + +
116A GLY* 4.5 8.5 - - - +
119A THR* 3.9 17.7 - - + -
120A ALA* 4.0 11.0 - - + -
123A PHE* 5.6 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A VAL* 3.5 15.8 + - + -
74A GLU* 4.3 4.0 - - - +
75A GLU 3.3 0.2 - - - -
76A VAL* 1.3 95.7 - - + +
78A ILE* 1.3 58.3 + - - +
80A LEU* 3.2 4.4 + - + +
81A ALA* 2.7 38.5 + - - +
82A GLY* 4.8 0.4 - - - -
85A VAL* 4.1 25.7 - - + +
87A LEU* 4.9 8.5 - - + -
106A LEU* 3.5 30.1 - - + -
112A VAL* 3.8 18.8 - - + -
113A LEU* 4.0 22.4 - - + -
116A GLY* 3.9 35.7 - - - -
117A GLU* 4.5 2.2 - - - -
120A ALA* 3.8 12.1 - - + -
293A MET* 5.7 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ARG* 3.9 22.9 - - - +
74A GLU* 3.1 25.2 + - + +
75A GLU* 3.1 21.5 + - - +
77A PHE* 1.3 77.0 - - - +
79A GLN* 1.3 66.5 + - - +
82A GLY* 3.1 32.3 + - - -
83A ASP 5.6 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PRO* 3.6 6.8 + - - +
26A VAL* 3.8 6.4 - - - +
27A ALA* 3.0 47.1 - - - +
30A LEU* 3.7 13.9 - - + -
38A VAL* 4.2 18.8 - - + +
75A GLU* 2.7 41.8 + - - +
76A VAL 3.5 9.6 - - - +
78A ILE* 1.3 81.5 - - - +
80A LEU* 1.3 62.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 4.2 16.6 - - + -
34A LEU* 3.9 27.8 - - + -
38A VAL* 4.4 14.4 - - + +
40A ALA* 4.0 34.6 - - + +
76A VAL* 3.2 17.4 + - + +
77A PHE* 3.2 7.4 + - + +
79A GLN* 1.3 81.3 - - - +
81A ALA* 1.3 63.3 + - + +
112A VAL* 4.8 13.2 - - + +
115A THR* 4.3 8.7 - - + -
116A GLY* 3.9 32.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE 2.7 13.0 + - - +
80A LEU* 1.3 76.5 - - - +
82A GLY* 1.3 71.7 + - - +
84A ASP* 3.1 24.9 + - + +
85A VAL* 3.7 15.1 + - + +
109A PRO* 5.6 1.6 - - + -
112A VAL* 4.1 22.4 - - + -
----------------------------------------------------------
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