Contacts of the strand formed by residues 37 - 46 (chain A) in PDB entry 3K8Y
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 GLU 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A THR* 3.6 0.8 - - - +
36A ILE* 1.3 85.8 - - + +
38A ASP* 1.3 70.2 + - - +
56A LEU* 3.7 38.0 - - + +
57A ASP 3.5 8.5 - - - +
58A THR* 4.6 4.0 - - - +
67A MET* 3.5 29.8 - - + +
70A GLN* 6.2 0.5 - - - +
71A TYR* 3.5 27.1 - - - +
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Residues in contact with ASP 38 (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 THR* 3.5 18.9 + - - +
36A ILE 5.4 0.3 + - - -
37A GLU* 1.3 85.1 + - - +
39A SER* 1.3 59.1 + - - +
40A TYR* 4.0 24.1 + - + +
56A LEU* 3.5 8.1 - - - +
57A ASP* 2.8 43.9 + - + +
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Residues in contact with SER 39 (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 ASP* 1.3 75.4 - - - +
40A TYR* 1.3 75.4 + - - +
41A ARG* 5.7 0.7 - - - +
54A ASP* 4.2 16.5 + - - -
55A ILE 3.4 7.0 + - - -
56A LEU* 4.5 10.9 - - - +
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Residues in contact with TYR 40 (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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17A SER* 5.7 0.2 - - - -
20A THR* 3.6 25.8 - - + -
21A ILE* 3.5 32.4 - - + +
24A ILE* 4.1 34.8 - - + -
25A GLN* 3.9 21.8 - - + -
38A ASP* 4.0 30.7 + - + +
39A SER* 1.3 84.4 + - - +
41A ARG* 1.3 60.6 + - - +
53A LEU 3.7 1.0 - - - +
54A ASP* 3.5 2.8 - - - -
55A ILE* 2.8 41.5 + - + +
57A ASP* 4.2 13.1 + - + -
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Residues in contact with ARG 41 (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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3A GLU* 3.7 18.2 + - - -
24A ILE* 5.0 4.8 - - - +
39A SER* 5.7 1.1 - - - +
40A TYR* 1.3 76.4 - - - +
42A LYS* 1.3 67.8 + - - +
52A LEU* 3.3 47.1 - - + +
53A LEU 3.2 5.4 - - - +
54A ASP* 4.4 15.8 + - - +
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Residues in contact with LYS 42 (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 LEU 4.2 7.4 + - - +
24A ILE* 3.1 56.5 + - + +
26A ASN* 4.2 11.1 - - - +
41A ARG* 1.3 77.7 - - - +
43A GLN* 1.3 74.9 + - - +
44A VAL* 3.7 15.9 + - + +
52A LEU* 3.9 5.2 - - - -
53A LEU* 2.9 36.7 + - + +
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Residues in contact with GLN 43 (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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1A MET* 3.4 26.1 - - - +
42A LYS* 1.3 82.4 - - - +
44A VAL* 1.3 69.5 + - - +
45A VAL* 6.3 0.4 - - + +
50A THR* 3.5 24.6 - - + +
51A CYS 3.3 12.6 - - - +
52A LEU* 4.0 11.3 - - + +
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Residues in contact with VAL 44 (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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42A LYS* 4.2 24.7 - - + +
43A GLN* 1.3 82.2 - - - +
45A VAL* 1.3 65.3 + - - +
46A ILE* 3.8 22.0 - - + -
49A GLU 3.7 0.5 - - - +
50A THR* 3.5 4.0 - - - +
51A CYS* 2.9 37.0 + - - +
53A LEU* 3.7 33.2 - - + -
157A TYR* 4.1 17.3 - - + +
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Residues in contact with VAL 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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43A GLN* 6.3 0.2 - - + -
44A VAL* 1.3 77.7 - - - +
46A ILE* 1.3 65.4 + - - +
47A ASP 4.1 0.9 + - - -
48A GLY* 3.7 33.0 - - - +
49A GLU 3.3 5.6 - - - +
50A THR* 3.8 20.0 - - + +
157A TYR* 4.2 10.9 + - - -
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Residues in contact with ILE 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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44A VAL* 3.8 23.3 - - + -
45A VAL* 1.3 77.0 - - - +
47A ASP* 1.3 85.2 + - - +
48A GLY 3.2 0.2 - - - -
49A GLU* 2.9 15.6 + - - +
51A CYS* 4.0 11.4 - - - -
53A LEU* 4.0 4.5 - - + -
157A TYR* 3.8 48.9 - - + +
160A VAL* 3.8 28.9 - - + -
161A ARG* 4.3 4.0 - - - +
164A ARG* 3.0 30.6 + - - +
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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