Contacts of the strand formed by residues 48 - 56 (chain A) in PDB entry 3A7H
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 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A ILE* 3.6 2.2 - - - -
43A ASP* 2.9 29.5 + - + +
46A THR* 3.2 17.9 - - - +
47A GLN* 1.3 79.8 - - - +
49A VAL* 1.3 82.0 + - - +
50A VAL* 3.6 5.7 + - + +
86A TYR* 5.0 13.5 + - + +
100A GLU* 6.0 3.2 - - - +
101A TYR 6.1 0.2 - - - +
118B GLU* 3.9 23.6 - - - -
242B ASN* 3.3 38.4 + - - +
243B TYR 4.1 0.2 - - - -
244B SER* 3.8 18.6 - - - +
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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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27A LEU* 5.4 0.7 - - + -
40A LYS* 3.8 30.3 - - + -
41A GLY 3.4 14.1 - - - +
42A ILE* 3.9 18.2 - - + -
47A GLN 5.6 0.9 - - - +
48A LYS* 1.3 93.7 + - + +
50A VAL* 1.3 68.3 + - - +
86A TYR* 5.5 1.7 - - - -
100A GLU* 5.5 0.2 - - - -
101A TYR* 3.9 26.4 + - + +
241B GLY 5.6 0.9 - - - +
242B ASN* 3.3 27.3 + - + +
243B TYR 5.0 6.5 - - - +
248B LYS* 6.0 2.0 - - - +
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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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24A PHE* 4.0 18.2 - - + -
40A LYS* 3.8 2.9 - - - -
41A GLY 2.9 43.0 + - - +
42A ILE 4.2 1.1 - - - +
43A ASP* 4.3 11.7 - - + +
48A LYS* 4.0 10.5 - - + +
49A VAL* 1.3 81.3 - - - +
51A ALA* 1.3 58.9 + - - +
52A ILE* 3.9 21.1 - - + -
86A TYR* 4.2 13.5 - - + -
98A ILE* 3.8 21.1 - - + -
99A MET 3.4 11.9 - - - +
101A TYR* 3.6 12.3 - - - +
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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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38A VAL* 4.6 3.1 - - + -
39A PHE 3.3 8.1 - - - +
50A VAL* 1.3 73.0 - - - +
52A ILE* 1.3 61.4 + - - +
97A ILE 3.7 0.7 - - - +
98A ILE* 3.6 3.8 - - - -
99A MET* 2.8 42.8 + - + +
100A GLU 3.8 1.8 - - - +
101A TYR* 3.7 9.7 - - + +
400A ATP 3.6 45.1 - - + +
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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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24A PHE* 3.8 28.5 - - + -
25A THR 4.8 0.7 - - - +
26A LYS* 4.5 11.9 - - + -
37A GLU 3.6 1.6 - - - +
38A VAL* 3.3 3.8 - - - +
39A PHE* 2.6 50.4 + - + +
41A GLY* 4.1 20.2 - - - +
50A VAL* 3.9 15.0 - - + +
51A ALA* 1.3 77.4 - - - +
53A LYS* 1.3 62.9 + - - +
54A ILE* 3.8 15.7 - - + -
96A TRP* 3.6 31.6 - - + -
97A ILE 3.6 2.5 - - - -
98A ILE* 4.1 13.9 - - + -
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Residues in contact with LYS 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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35A PHE* 3.4 25.4 - - - -
36A GLY 5.4 0.7 - - - +
37A GLU 3.4 10.3 - - - +
38A VAL* 4.2 10.3 - - + +
51A ALA 4.1 0.6 - - - -
52A ILE* 1.3 73.0 - - - +
54A ILE* 1.3 60.9 + - - +
55A ILE* 3.6 30.7 + - + -
67A ILE* 5.6 0.6 - - - +
70A GLU* 4.5 15.0 + - - -
95A LEU 3.4 1.7 - - - +
96A TRP* 3.3 1.6 - - - -
97A ILE* 2.6 59.4 + - + +
99A MET* 3.8 24.2 - - + -
400A ATP 2.8 38.9 + - - +
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Residues in contact with ILE 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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26A LYS* 3.5 36.6 - - + +
36A GLY* 3.3 4.2 - - - -
37A GLU* 2.9 32.5 + - + +
39A PHE* 4.4 12.6 - - + -
52A ILE* 3.8 16.2 - - + +
53A LYS* 1.3 75.6 - - - +
55A ILE* 1.3 65.6 + - - +
94A LYS* 4.0 32.5 - - + -
95A LEU 3.2 4.7 - - - +
96A TRP* 3.5 30.1 - - + +
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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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35A PHE* 3.3 43.3 - - + +
36A GLY* 4.4 0.4 - - - +
53A LYS* 3.6 27.4 - - + -
54A ILE* 1.3 80.4 - - - +
56A ASP* 1.3 70.6 + - - +
57A LEU* 3.5 4.1 + - + +
60A ALA* 5.0 7.2 - - + -
64A ILE* 6.4 0.2 - - + -
67A ILE* 3.4 39.9 - - + -
94A LYS* 3.3 5.6 - - - -
95A LEU* 2.8 43.3 + - + +
97A ILE* 4.3 11.4 - - + -
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Residues in contact with ASP 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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35A PHE 4.7 2.2 + - - -
36A GLY* 5.5 0.4 - - - -
55A ILE* 1.3 78.1 - - - +
57A LEU* 1.3 60.2 + - - +
58A GLU* 2.9 20.8 + - - +
59A GLU* 3.2 48.6 + - + +
60A ALA* 3.5 17.2 + - - +
93A THR* 2.9 24.1 + - - -
94A LYS* 3.0 29.2 - - + +
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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