Contacts of the helix formed by residues 81 - 94 (chain A) in PDB entry 1QDV
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 ASN 81 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 3.6 7.9 - - - +
80A ARG* 1.3 76.9 - - - +
82A ARG* 1.3 63.8 + - - +
83A PRO* 3.5 20.4 - - - +
84A SER* 2.9 41.1 + - - +
85A PHE* 3.8 10.4 + - - +
104A VAL* 4.2 4.0 - - - +
108A ILE* 4.2 13.5 - - + +
112A GLU* 4.4 12.5 + - - +
116A TYR* 5.3 1.0 + - - -
86D ASP* 4.6 14.1 + - - +
90D TYR* 4.1 30.3 - - + +
93D GLN* 4.1 7.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 3.2 28.3 - - + +
40A SER* 2.8 38.3 + - - -
42A LEU* 3.4 45.4 - - + +
44A PHE* 4.2 3.1 - - - -
80A ARG 3.3 0.4 + - - +
81A ASN* 1.3 68.4 - - - +
83A PRO* 1.3 77.1 - - + +
84A SER 3.1 1.6 - - - -
85A PHE* 3.0 17.3 + - - +
86A ASP* 3.4 9.6 - - - +
42D LEU* 3.7 33.9 - - - +
43D ARG 2.8 26.6 + - - -
44D PHE* 3.5 33.8 - - - +
86D ASP* 3.7 6.2 + - - +
89D LEU* 5.1 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ASN* 3.5 19.5 - - - +
82A ARG* 1.3 96.7 - - + +
84A SER* 1.3 60.5 + - - +
86A ASP* 3.5 16.0 + - - +
101A PRO* 3.6 17.8 - - + +
103A ASN* 5.7 7.4 - - + +
104A VAL* 3.7 18.6 - - + -
86D ASP* 3.5 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ASN* 2.9 28.2 + - - -
82A ARG 3.1 0.4 - - - -
83A PRO* 1.3 77.4 - - - +
85A PHE* 1.3 66.0 + - - +
87A ALA* 3.2 10.9 + - - +
88A ILE* 3.3 12.7 + - - +
101A PRO* 4.5 0.4 - - - -
104A VAL* 3.4 21.5 - - - +
108A ILE* 4.3 0.9 - - - +
109A PHE* 3.6 22.1 - - - -
112A GLU* 3.6 31.5 - - - +
116A TYR* 6.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 3.9 26.0 - - + -
39A ILE* 3.6 19.7 - - + -
44A PHE* 3.5 39.3 - + + -
59A LEU* 3.8 22.9 - - + -
81A ASN 3.8 6.8 + - - +
82A ARG 3.0 13.6 + - - +
84A SER* 1.3 76.7 - - - +
86A ASP* 1.3 67.3 + - - +
88A ILE* 3.0 22.3 + - + -
89A LEU* 2.9 40.7 + - + +
116A TYR* 3.5 37.9 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 4.9 2.8 - - - +
44A PHE* 3.6 20.1 - - + -
82A ARG 3.4 15.6 - - - +
83A PRO* 3.5 13.3 - - - +
84A SER 3.3 0.6 - - - -
85A PHE* 1.3 73.2 - - - +
87A ALA* 1.3 58.4 + - - +
89A LEU* 3.4 2.7 + - - +
90A TYR* 2.9 30.0 + - - +
93A GLN* 5.1 0.2 - - - +
101A PRO* 6.0 0.9 - - + -
82B ARG* 2.7 43.9 + - + +
83B PRO* 5.0 9.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PRO 4.7 0.8 + - - -
84A SER 3.2 9.5 + - - +
85A PHE 3.1 0.6 - - - -
86A ASP* 1.3 79.1 - - - +
88A ILE* 1.3 60.6 + - - +
90A TYR* 3.8 8.3 - - - +
91A TYR* 3.0 26.9 + - - +
97A ARG 4.5 2.4 - - - +
98A LEU* 4.4 4.3 - - - +
99A ARG 3.2 28.2 + - - +
101A PRO* 3.8 17.2 - - + +
109A PHE* 3.8 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 4.5 1.3 - - + -
84A SER 3.5 14.1 - - - +
85A PHE* 3.0 31.3 + - + +
87A ALA* 1.3 75.7 - - - +
89A LEU* 1.3 63.6 + - - +
91A TYR* 3.1 21.2 + - - +
92A TYR* 3.2 26.1 - - + -
98A LEU* 4.6 0.7 - - + -
109A PHE* 4.2 21.3 - - + -
112A GLU* 4.6 3.8 - - + +
113A ILE* 4.5 12.1 - - + +
116A TYR* 4.0 37.0 - - + -
118A LEU* 4.1 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 5.2 1.3 - - + -
44A PHE* 4.1 29.4 - - + -
45A GLU 4.4 6.7 - - - +
46A THR* 3.8 32.1 - - + +
50A THR* 4.7 2.7 - - + -
51A LEU* 4.4 13.7 - - + -
59A LEU* 6.3 0.2 - - + -
85A PHE* 2.9 31.0 + - + +
86A ASP* 3.8 4.5 - - - +
88A ILE* 1.3 77.5 - - - +
90A TYR* 1.3 62.5 + - - +
92A TYR* 3.0 19.5 + - + +
93A GLN* 3.1 35.3 + - + +
40B SER* 4.1 13.9 - - - -
82B ARG* 5.3 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ASP 2.9 18.5 + - - +
87A ALA* 3.9 8.3 - - - +
88A ILE 3.3 0.2 - - - -
89A LEU* 1.3 73.4 - - - +
91A TYR* 1.3 64.9 + - - +
93A GLN* 3.3 21.7 + - + +
94A SER* 2.8 53.3 + - - -
97A ARG* 2.9 42.1 + - + -
99A ARG* 5.7 2.9 - - + -
81B ASN* 3.5 44.4 - - + +
108B ILE* 3.5 34.7 - - + +
111B GLU* 3.9 4.9 + - - -
112B GLU* 4.9 6.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A PHE* 3.4 47.1 - + + -
57A THR* 5.1 0.2 - - + -
87A ALA 3.0 14.2 + - - +
88A ILE* 3.2 10.3 - - - +
90A TYR* 1.3 76.8 - - - +
92A TYR* 1.3 67.5 + + - +
95A GLY 3.3 1.2 + - - -
96A GLY* 2.9 61.2 + - - -
97A ARG 3.2 15.4 + - - +
98A LEU* 3.8 26.0 - - + -
118A LEU* 3.9 38.7 + - + -
122A ALA* 3.7 26.5 - - + +
125A MET* 5.9 2.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A THR* 3.5 31.2 - - + +
51A LEU* 3.5 31.4 - - + -
53A GLN* 2.5 27.1 + - - +
54A PHE* 3.8 24.2 - + + -
57A THR* 2.7 36.8 + - + +
59A LEU* 3.7 33.4 + - + +
60A GLY 4.7 1.3 - - - -
88A ILE* 3.2 34.5 - - + -
89A LEU* 3.0 12.8 + - + +
91A TYR* 1.3 83.0 - + - +
93A GLN* 1.3 62.1 + - - +
95A GLY* 3.1 9.4 + - - -
116A TYR* 4.5 1.2 + - - +
118A LEU* 3.9 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A THR* 3.9 14.8 - - + -
53A GLN* 4.3 6.6 + - - +
86A ASP 5.1 0.2 - - - +
89A LEU* 3.1 26.2 + - + +
90A TYR* 3.3 35.6 + - + +
92A TYR* 1.3 76.9 - - - +
94A SER* 1.3 60.3 + - - +
95A GLY 3.6 0.2 + - - -
40B SER* 2.8 27.9 + - - -
79B ASP* 2.9 43.0 + - - +
80B ARG* 3.8 9.4 - - - +
81B ASN* 4.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TYR* 2.8 49.2 + - - -
91A TYR 3.4 0.7 + - - -
93A GLN* 1.3 76.3 - - - +
95A GLY* 1.3 59.8 + - - +
96A GLY 3.7 0.2 + - - -
97A ARG* 3.0 41.7 + - - +
111B GLU* 5.7 0.2 - - - -
----------------------------------------------------------
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