Contacts of the strand formed by residues 44 - 50 (chain A) in PDB entry 1QAD
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 TYR 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A VAL* 4.7 2.0 - - + -
36A ARG 3.4 5.6 - - - +
37A GLU* 3.5 41.1 + - + -
42A GLY 3.5 4.2 + - - +
43A CYS* 1.3 106.8 - - + +
45A ALA* 1.3 64.1 + - - +
58A VAL* 3.8 8.5 - - - +
59A ILE* 3.1 44.2 + - + +
61A LYS* 3.8 25.2 + - + +
66A TYR* 3.8 24.7 + + - -
78A LEU* 3.8 22.8 - - + +
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Residues in contact with ALA 45 (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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35A VAL* 3.4 6.2 - - - +
36A ARG* 2.9 69.2 + - + +
44A TYR* 1.3 79.6 - - - +
46A CYS* 1.3 60.6 + - - +
57A CYS 3.4 16.2 - - - +
58A VAL* 4.6 2.0 - - + -
59A ILE* 3.8 8.7 - - - +
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Residues in contact with CYS 46 (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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33A PHE* 4.6 2.9 - - - -
34A LEU 3.5 11.2 - - - -
35A VAL* 5.1 1.8 - - + -
45A ALA* 1.3 75.1 - - - +
47A SER* 1.3 73.0 + - - +
48A VAL* 4.3 8.3 - - - +
55A LYS 3.9 0.2 - - - +
56A HIS* 3.3 4.5 - - - +
57A CYS* 2.9 37.4 + - - +
59A ILE* 4.0 7.8 - - + +
68A PHE* 3.9 28.7 - - + -
90A LEU* 5.1 1.1 - - - -
101A LEU* 3.7 33.4 - - - -
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Residues in contact with SER 47 (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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21A ALA* 3.4 10.7 - - - +
25A LEU* 3.6 22.2 - - - +
33A PHE* 3.1 3.8 - - - +
34A LEU* 2.9 39.7 + - - +
36A ARG* 3.0 20.1 + - - -
46A CYS* 1.3 71.4 - - - +
48A VAL* 1.3 61.8 + - - +
55A LYS 3.2 4.9 - - - -
56A HIS* 2.8 29.4 + - - -
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Residues in contact with VAL 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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25A LEU* 4.1 2.1 - - - +
31A GLY 4.3 5.6 - - - -
32A THR 3.3 12.8 - - - +
33A PHE* 3.9 13.2 - - + -
46A CYS* 4.3 16.4 - - - +
47A SER* 1.3 76.0 - - - +
49A VAL* 1.3 76.7 + - - +
50A VAL* 3.6 11.9 + - + -
54A VAL* 4.6 0.9 - - - -
55A LYS* 2.9 37.6 + - + +
56A HIS 6.3 0.2 - - - -
57A CYS* 5.8 2.0 - - - -
90A LEU* 5.0 5.8 - - + -
97A LEU* 4.9 6.5 - - + -
99A VAL* 4.0 25.8 - - + -
100A THR 4.5 0.4 - - - +
101A LEU* 4.3 8.3 - - + -
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Residues in contact with VAL 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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25A LEU* 3.9 37.5 - - + +
28A LYS 3.5 18.2 - - - +
29A ARG 3.6 15.3 - - - +
30A ASP* 3.5 19.8 - - - +
31A GLY 2.8 25.8 + - - -
32A THR* 3.0 16.1 + - - +
48A VAL* 1.3 72.9 - - - +
50A VAL* 1.3 61.9 + - - +
52A GLY* 4.4 4.3 - - - -
53A GLU 3.5 19.1 - - - +
54A VAL* 4.2 7.4 - - + -
99A VAL* 3.7 5.5 - - - +
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Residues in contact with VAL 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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30A ASP* 4.5 1.6 - - - -
48A VAL* 3.8 13.0 - - + +
49A VAL* 1.3 78.7 - - - +
51A ASP* 1.3 86.6 + - - +
52A GLY 3.2 0.9 - - - -
53A GLU* 2.9 24.6 + - - +
55A LYS* 4.0 25.1 - - + +
96A SER 3.6 16.4 - - - +
97A LEU* 4.2 10.3 - - + -
98A ASN* 4.1 23.8 - - + +
99A VAL* 3.9 22.7 - - + -
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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