Contacts of the helix formed by residues 51 - 64 (chain A) in PDB entry 1QHP
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 51 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 3.8 27.4 - - + -
50A ASP* 1.3 72.3 - - - +
52A GLU* 1.3 65.5 + - - +
54A VAL* 3.2 6.4 + - - +
55A ARG* 3.0 21.4 + - - +
71A LEU* 4.1 11.0 - - + -
74A VAL* 4.3 7.2 - - + -
100A ILE* 4.0 24.7 - - + -
104A PHE* 3.0 24.4 + - + +
109A THR* 4.0 14.1 - - + +
110A PHE* 4.1 29.2 - - + +
113A LEU* 3.8 28.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLY* 3.8 11.4 - - - +
23A ASP* 4.5 11.4 - - + +
50A ASP* 3.3 7.7 + - - +
51A LEU* 1.3 78.7 - - - +
53A GLY* 1.3 55.5 + - - +
55A ARG* 2.8 44.1 + - - +
56A GLN* 2.8 60.9 + - - +
104A PHE 4.3 0.2 + - - -
109A THR* 3.9 20.2 - - + +
112A THR* 5.2 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TYR* 3.2 35.3 - - - -
22A GLY* 3.5 11.9 - - - -
50A ASP* 2.8 16.2 + - - -
52A GLU* 1.3 69.8 - - - +
54A VAL* 1.3 65.7 + - - +
56A GLN* 3.3 3.1 + - - +
57A LYS* 3.2 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 4.1 31.4 - - + -
16A ILE* 4.8 5.8 - - + -
19A PHE* 4.1 23.1 - - + -
20A TYR 4.5 0.2 + - - -
50A ASP 3.2 13.6 + - - +
51A LEU* 3.2 11.1 + - - +
53A GLY* 1.3 75.6 - - - +
55A ARG* 1.3 64.2 + - - +
57A LYS* 3.0 14.4 + - - +
58A LEU* 3.4 10.6 + - - +
61A LEU* 4.5 3.5 - - + +
69A ILE* 4.3 15.5 - - + -
71A LEU* 4.3 14.1 - - + -
113A LEU* 3.7 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU 3.0 10.9 + - - +
52A GLU* 2.8 46.9 + - - +
54A VAL* 1.3 77.6 - - - +
56A GLN* 1.3 72.0 + - - +
58A LEU* 3.3 22.5 + - + +
59A PRO* 4.5 1.6 - - - +
112A THR* 3.6 27.7 - - - +
113A LEU* 3.6 22.8 - - + +
116A ASP* 3.1 42.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TYR* 3.5 24.8 + - + -
22A GLY* 3.1 30.4 + - - +
52A GLU* 2.8 44.1 + - - +
53A GLY* 3.7 6.1 - - - +
54A VAL 3.2 0.2 - - - -
55A ARG* 1.3 84.0 - - - +
57A LYS* 1.3 64.2 + - + +
58A LEU 3.4 0.8 + - - -
59A PRO* 3.8 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 3.8 21.3 - - + -
20A TYR* 3.7 32.1 + - + -
53A GLY 3.2 14.8 + - - +
54A VAL 3.0 8.7 + - - +
56A GLN* 1.3 82.7 - - + +
58A LEU* 1.3 63.1 + - - +
59A PRO* 3.4 2.9 - - - -
60A TYR* 3.1 12.0 + - + +
61A LEU* 3.1 23.3 + - + +
382A PHE* 3.6 56.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL 3.4 8.7 + - - +
55A ARG* 3.3 24.4 + - + +
57A LYS* 1.3 75.6 - - - +
59A PRO* 1.3 64.5 - - + +
61A LEU* 3.2 5.8 + - + +
62A LYS* 2.8 32.4 + - - +
69A ILE* 3.9 27.4 - - + -
113A LEU* 4.4 5.4 - - + +
116A ASP* 3.6 20.6 - - + +
117A ALA* 3.5 38.4 - - + +
120A ASN* 4.0 17.0 - - + +
122A ILE* 4.2 14.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ARG 4.5 1.1 - - - +
56A GLN 3.8 12.8 - - - +
57A LYS* 3.4 4.5 - - - -
58A LEU* 1.3 95.7 - - + +
60A TYR* 1.3 60.0 + - - +
62A LYS* 3.4 6.2 + - + +
63A GLN* 3.0 40.2 + - - +
120A ASN* 5.5 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TYR* 4.3 0.2 - - - -
19A PHE* 4.9 1.6 - + - -
57A LYS* 3.1 19.5 + - + +
59A PRO* 1.3 80.2 - - - +
61A LEU* 1.3 78.7 + - + +
63A GLN* 3.3 12.3 + - - +
64A LEU* 2.9 32.3 + - + +
364A GLU* 2.6 34.2 + - + +
365A GLN* 2.9 19.0 + - - -
379A MET* 3.7 16.1 - - + +
382A PHE* 3.5 52.0 - + + -
383A ASP 4.3 0.2 - - - -
384A THR* 4.0 5.4 - - + -
389A PHE* 3.5 25.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TYR* 3.5 38.8 - - + -
14A ILE* 4.3 13.0 - - + -
19A PHE* 4.2 8.5 - - + -
54A VAL* 4.5 6.7 - - + +
57A LYS 3.1 20.6 + - - +
58A LEU* 3.7 10.5 - - + +
60A TYR* 1.3 88.6 - - + +
62A LYS* 1.3 66.2 + - - +
64A LEU* 3.3 4.9 + - - +
65A GLY 3.3 4.0 + - - -
66A VAL* 3.0 41.0 + - + +
69A ILE* 3.9 27.1 - - + -
122A ILE* 4.4 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU 2.8 21.5 + - - +
59A PRO* 3.7 7.0 - - + +
61A LEU* 1.3 73.2 - - - +
63A GLN* 1.3 62.4 + - + +
65A GLY* 3.0 15.1 + - - -
66A VAL 4.5 4.2 - - - +
120A ASN* 2.8 47.8 + - + +
121A GLY* 4.8 3.0 - - - -
122A ILE* 4.0 15.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PRO* 3.0 39.6 + - - +
60A TYR* 3.6 10.2 - - - +
62A LYS* 1.3 78.3 - - + +
64A LEU* 1.3 57.1 + - - +
65A GLY* 3.4 0.3 + - - -
384A THR* 3.8 24.7 + - - +
389A PHE* 3.6 14.8 - - + -
393A SER* 3.0 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TYR* 3.6 32.5 - - + -
60A TYR* 2.9 21.5 + - + +
61A LEU* 3.5 9.9 - - + +
62A LYS 3.3 0.2 - - - -
63A GLN* 1.3 76.2 - - - +
65A GLY* 1.3 55.5 + - - +
66A VAL* 3.8 13.7 - - + -
359A ILE* 5.9 1.3 - - + -
364A GLU* 3.7 19.7 - - + +
389A PHE* 3.4 40.1 - - + +
392A VAL* 3.4 32.3 - - + +
393A SER* 3.1 23.7 + - - -
----------------------------------------------------------
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