Contacts of the helix formed by residues 47 - 57 (chain A) in PDB entry 1QVA
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 ILE 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A ILE* 3.5 26.9 - - + -
45A SER* 3.3 5.1 + - - +
46A ALA* 1.3 79.1 - - + +
48A GLN* 1.3 54.1 + - - +
50A ARG* 3.1 4.3 + - - +
51A ALA* 2.6 44.2 + - + +
63A ALA* 5.4 4.9 - - + -
64A GLN 4.2 13.0 - - - +
65A ALA* 4.0 27.6 - - + -
70A GLY* 4.7 5.6 - - - +
71A LYS* 4.8 4.5 - - + +
74A THR* 3.2 23.1 - - + +
199A LEU* 6.4 1.1 - - + -
221A ILE* 4.6 16.2 - - + -
223A VAL* 5.3 3.4 - - - +
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Residues in contact with GLN 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 3.9 12.8 - - - -
26A MET* 3.9 2.8 - - - +
41A PHE* 3.7 15.4 - - - -
43A GLU 4.3 2.0 + - - -
44A PRO* 3.2 17.8 - - + +
45A SER* 2.6 48.6 + - - +
47A ILE* 1.3 74.5 - - - +
49A GLN* 1.3 62.0 + - - +
50A ARG 3.0 5.4 + - - -
52A ILE* 3.4 43.1 + - + +
53A MET 5.0 0.2 + - - -
69A THR* 3.5 12.8 - - - +
70A GLY* 3.1 15.3 - - - +
73A GLY* 4.0 7.3 - - - -
74A THR* 3.2 22.2 - - - +
77A ILE* 4.6 1.1 - - - +
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Residues in contact with GLN 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LYS 4.2 1.2 - - - +
19A VAL* 3.5 14.8 - - + -
20A VAL* 3.0 49.5 + - - +
21A TYR* 3.5 33.8 + - + +
26A MET* 4.7 0.7 - - - -
43A GLU* 4.7 7.7 + - - -
44A PRO* 3.1 27.6 + - + +
45A SER 2.8 29.4 + - - +
46A ALA* 3.9 10.5 - - - +
47A ILE 3.3 0.4 - - - -
48A GLN* 1.3 73.7 - - - +
50A ARG* 1.3 76.4 + - - +
53A MET* 5.8 2.4 - - - +
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Residues in contact with ARG 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ILE* 4.0 36.2 - - - +
14A THR* 4.5 18.4 - - + +
16A TYR* 4.2 8.9 - - + +
18A LYS 4.8 4.5 - - - -
19A VAL* 4.1 26.2 - - + +
21A TYR* 5.2 4.6 + - - -
46A ALA* 2.9 29.8 + - - +
47A ILE 3.1 6.1 + - - +
49A GLN* 1.3 106.8 + - - +
51A ALA* 1.3 59.0 + - - +
52A ILE 3.7 0.9 - - - -
53A MET 5.1 0.4 - - - -
54A PRO* 3.1 23.4 - - - +
221A ILE* 3.6 18.5 - - + +
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Residues in contact with ALA 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ILE* 2.6 27.1 + - + +
50A ARG* 1.3 76.1 - - - +
52A ILE* 1.3 60.6 + - - +
54A PRO* 3.2 9.2 - - - +
55A ILE* 3.1 27.2 - - + +
61A VAL* 5.1 2.6 - - + +
63A ALA* 4.7 8.5 - - + -
74A THR* 3.5 22.9 - - + -
221A ILE* 3.5 20.4 - - + -
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Residues in contact with ILE 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 4.0 13.7 - - + -
26A MET* 3.7 33.4 - - + -
48A GLN* 3.4 37.4 + - + +
50A ARG 3.7 0.2 - - - -
51A ALA* 1.3 77.0 - - - +
53A MET* 1.3 60.2 + - - +
55A ILE* 3.4 3.6 + - - +
56A ILE* 3.0 49.3 + - + +
74A THR* 4.0 26.2 - - - +
77A ILE* 4.1 23.3 - - + -
78A ALA* 4.1 3.5 - - + +
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Residues in contact with MET 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A TYR* 3.9 10.1 - - + +
18A LYS* 5.8 4.3 - - + +
20A VAL* 3.8 27.1 - - + -
25A ASP 5.2 1.8 - - - +
26A MET* 3.5 53.2 - - + +
27A GLU* 5.0 9.0 - - + +
48A GLN 5.0 0.6 + - - -
49A GLN 5.8 2.4 + - - +
50A ARG 5.1 0.8 - - - -
52A ILE* 1.3 71.9 - - + +
54A PRO* 1.3 75.4 - - + +
56A ILE* 3.7 22.3 - - + +
57A GLU* 3.0 51.0 + - + +
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Residues in contact with PRO 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A TYR* 3.7 28.0 - - + -
50A ARG 3.1 28.5 - - - +
51A ALA* 3.2 16.6 - - - +
53A MET* 1.3 94.7 - - + +
55A ILE* 1.3 60.8 + - - +
57A GLU* 3.3 13.7 + - - +
59A HIS* 3.3 29.8 + - - +
61A VAL* 4.3 3.4 - - + -
219A VAL* 4.0 28.0 - - + -
221A ILE* 4.9 0.4 - - + -
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Residues in contact with ILE 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ALA* 3.1 20.4 - - + +
52A ILE 3.4 1.7 + - - +
53A MET 3.2 0.6 - - - -
54A PRO* 1.3 72.7 - - - +
56A ILE* 1.3 68.3 + - - +
57A GLU 2.9 1.3 - - - -
58A GLY 2.8 13.5 + - - -
61A VAL* 3.8 22.0 - - + -
74A THR* 3.8 23.3 - - + +
75A PHE* 4.4 5.8 - - - -
78A ALA* 3.5 27.8 - - + -
82A ARG* 4.0 1.7 - - - -
165A MET* 3.7 23.3 - - + -
195A GLN* 2.9 26.0 + - - +
197A VAL* 4.1 23.8 - - + -
199A LEU* 5.8 1.3 - - + -
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Residues in contact with ILE 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A MET 4.5 2.5 - - - +
28A LEU* 4.0 18.6 - - + -
52A ILE* 3.0 37.8 + - + +
53A MET* 3.7 30.3 - - + +
55A ILE* 1.3 80.2 - - - +
57A GLU* 1.3 63.2 + - + +
58A GLY 3.4 0.9 + - - -
77A ILE* 5.5 0.4 - - + +
78A ALA* 4.0 18.2 - - - -
81A GLN* 3.9 28.0 - - + +
82A ARG* 3.8 23.2 + - + +
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Residues in contact with GLU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A TYR* 2.7 33.7 + - - -
18A LYS* 5.4 6.2 + - - +
53A MET* 3.0 39.5 + - + +
54A PRO 3.7 4.7 - - - +
55A ILE 2.8 1.8 + - - -
56A ILE* 1.3 82.3 - - + +
58A GLY* 1.3 56.3 + - - -
59A HIS* 3.5 20.9 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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