Contacts of the strand formed by residues 56 - 64 (chain D) in PDB entry 3LAW
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 LEU 56 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5D LYS 3.5 11.8 + - - +
6D LYS* 3.4 27.3 - - + -
7D VAL* 3.4 18.4 + - - +
49D GLU* 3.3 39.7 - - + +
50D VAL 3.9 7.0 - - - +
51D MET* 3.5 28.8 - - + -
55D ARG* 1.3 73.6 + - - +
57D VAL* 1.3 70.2 + - - +
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Residues in contact with VAL 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LYS* 5.2 0.2 - - - +
7D VAL* 3.6 9.0 - - + +
9D LEU* 3.5 26.9 - - + -
48D LYS 3.8 0.2 - - - +
49D GLU* 3.2 6.6 - - - +
50D VAL* 3.0 45.1 + - + +
52D VAL* 4.3 12.3 - - + -
55D ARG* 3.9 11.0 - - + +
56D LEU* 1.3 82.0 - - - +
58D THR* 1.3 72.1 + - - +
59D MET* 4.2 11.4 - - + -
170D ALA* 5.0 0.9 - - + -
174D LEU* 3.9 30.5 - - + -
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Residues in contact with THR 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ASN* 5.0 6.5 - - - +
129B PHE* 3.4 36.4 - - + -
157B LYS* 4.8 4.0 + - - +
1400B GNP 5.6 2.0 - - - +
6D LYS* 4.9 4.2 - - - +
7D VAL 2.8 9.3 + - - -
8D LEU* 3.8 7.2 - - + +
9D LEU 2.9 27.4 + - - +
47D THR* 4.4 20.9 - - + +
48D LYS 3.6 5.6 - - - +
49D GLU* 3.7 26.5 + - + +
57D VAL* 1.3 77.8 - - - +
59D MET* 1.3 61.5 + - - +
60D GLN 3.4 1.4 + - - +
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Residues in contact with MET 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LEU* 3.7 8.7 - - + -
11D VAL* 3.8 22.9 - - + -
28D TYR* 3.6 9.4 - - + +
46D LEU 3.6 0.5 - - - +
47D THR* 3.1 5.0 - - - -
48D LYS* 2.6 44.8 + - + +
50D VAL* 4.3 12.1 - - + -
57D VAL* 3.8 14.8 + - + -
58D THR* 1.3 71.2 - - - +
60D GLN* 1.3 61.4 + - - +
61D ILE* 3.6 25.3 + - + +
166D PHE* 3.2 40.2 - - + +
169D ILE* 4.6 1.3 - - + -
170D ALA* 3.9 27.8 - - - -
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Residues in contact with GLN 60 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B GLY* 5.5 1.0 + - - -
126B LYS* 5.0 9.3 - - - +
1400B GNP 4.8 6.1 - - - -
8D LEU* 4.4 24.7 - - + +
9D LEU 2.9 13.5 + - - +
10D LYS* 3.9 15.3 - - - +
11D VAL* 2.8 32.1 + - - +
45D PHE* 3.3 47.4 - - + -
46D LEU 3.9 2.0 - - - -
47D THR* 4.0 10.9 - - + +
58D THR* 3.4 2.6 + - + -
59D MET* 1.3 71.0 - - - +
61D ILE* 1.3 58.9 - - - +
62D TRP* 3.5 24.4 + - - +
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Residues in contact with ILE 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D VAL* 3.5 7.9 - - + +
13D ILE* 3.3 34.8 - - + -
25D MET* 3.5 22.1 - - + +
28D TYR* 3.7 22.9 - - + -
29D VAL* 4.1 15.5 - - + -
45D PHE* 3.1 6.5 - - - -
46D LEU 2.7 37.5 + - - +
48D LYS* 5.0 1.3 - - + -
59D MET* 3.6 42.0 - - + +
60D GLN* 1.3 77.4 - - - +
62D TRP* 1.3 59.6 - - - +
166D PHE* 4.0 6.5 - - + -
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Residues in contact with TRP 62 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67B GLN* 5.9 5.4 - - - -
69B ARG* 5.7 1.6 - - - -
10D LYS* 3.2 49.2 - - + +
11D VAL 2.8 17.7 + - - +
12D ILE* 3.9 17.4 - - + +
13D ILE* 3.0 28.3 + - - +
43D ALA* 4.1 25.4 - - + -
44D ASP* 3.4 23.6 - - - -
45D PHE* 3.4 34.1 - + + -
60D GLN* 3.5 21.3 + - - -
61D ILE* 1.3 74.4 - - - +
63D ASP* 1.3 61.5 + - - +
64D THR 3.9 0.5 + - - -
77D PHE* 4.3 28.3 - + + -
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Residues in contact with ASP 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ILE* 4.8 4.7 - - - +
21D LYS* 4.0 13.7 - - - +
22D THR* 2.7 43.7 + - - +
25D MET* 3.7 23.6 - - + +
40D THR* 3.6 8.6 + - + +
43D ALA* 3.1 27.2 - - - +
44D ASP* 3.0 16.2 + - + +
61D ILE 3.7 2.4 + - - -
62D TRP* 1.3 73.0 - - - +
64D THR* 1.3 78.2 + - - +
1401D MG 3.2 8.2 - - - -
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Residues in contact with THR 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ILE* 4.1 13.0 - - + -
13D ILE 2.7 24.4 + - - +
14D LEU* 3.7 14.9 - - + +
21D LYS* 3.7 9.2 - - - -
40D THR* 4.0 3.1 - - - -
42D GLY 3.4 4.7 - - - -
43D ALA* 4.2 3.1 - - + -
62D TRP 3.9 0.8 + - - -
63D ASP* 1.3 91.3 + - - +
65D ALA* 1.3 69.7 + - - +
66D GLY 3.5 1.0 + - - -
71D GLN* 6.4 0.4 - - - -
77D PHE* 3.4 38.6 - - + -
78D TYR* 5.3 0.4 - - + -
1401D MG 3.2 11.1 - - - -
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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