Contacts of the strand formed by residues 44 - 52 (chain A) 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 ASP 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A MET* 5.9 0.4 - - - -
40A THR* 5.5 2.0 - - - +
41A ILE 5.1 1.8 + - - +
43A ALA* 1.3 74.5 - - - +
45A PHE* 1.3 79.6 + - - +
62A TRP* 3.2 16.5 - - - -
63A ASP* 3.0 29.3 + - - +
37C TYR* 3.0 38.5 - - - +
38C LYS* 5.7 0.7 - - - -
39C ALA* 5.6 2.7 + - - +
67C GLN* 5.3 3.0 - - - +
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Residues in contact with PHE 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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25A MET* 5.0 2.2 - - - -
44A ASP* 1.3 102.2 + - - +
46A LEU* 1.3 81.0 + - - +
47A THR* 3.6 16.4 - - + -
60A GLN* 3.3 38.8 - - + -
61A ILE 3.1 20.0 - - - +
62A TRP* 3.6 36.6 - + + -
63A ASP 4.5 0.2 - - - +
18C GLY* 5.6 6.3 - - - -
37C TYR* 3.2 53.5 + + + +
1400C GNP 3.8 10.8 - - - -
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Residues in contact with LEU 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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25A MET* 3.3 37.2 - - + -
26A ASN* 4.1 19.7 - - - +
29A VAL* 4.1 23.8 - - + -
30A ASN* 4.2 16.2 - - - +
45A PHE* 1.3 84.7 - - - +
47A THR* 1.3 63.3 + - - +
59A MET 3.5 1.0 - - - +
60A GLN 3.5 0.2 - - - -
61A ILE* 2.6 41.8 + - - +
36C GLN* 5.7 11.4 - - + +
37C TYR 5.7 5.6 - - - +
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Residues in contact with THR 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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29A VAL* 3.9 15.6 - - - +
45A PHE* 3.6 18.6 - - + -
46A LEU* 1.3 74.5 - - - +
48A LYS* 1.3 60.6 + - - +
49A GLU 5.3 0.2 + - - -
58A THR* 4.3 17.3 - - + +
59A MET 3.2 7.2 - - - -
60A GLN* 4.4 8.5 - - + +
35C ASN* 3.4 38.3 + - + +
36C GLN* 5.8 2.4 - - - +
37C TYR 5.2 0.9 - - - +
1400C GNP 3.6 24.7 - - - +
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Residues in contact with LYS 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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28A TYR* 2.8 68.4 + - + +
29A VAL* 4.0 30.9 + - + +
31A LYS* 6.0 2.9 - - - +
46A LEU 4.1 0.8 + - - -
47A THR* 1.3 75.5 - - - +
49A GLU* 1.3 79.8 + - - +
50A VAL* 3.9 2.8 + - + +
58A THR* 3.8 1.9 - - - -
59A MET* 2.8 36.5 + - + +
61A ILE* 4.4 4.9 - - + +
163A GLU* 4.5 3.8 + - - -
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Residues in contact with GLU 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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47A THR* 5.3 0.4 + - - -
48A LYS* 1.3 89.0 - - - +
50A VAL* 1.3 60.5 + - - +
56A LEU* 4.0 26.4 - - + +
57A VAL 3.3 9.6 - - - +
58A THR* 3.5 27.4 + - + +
35C ASN* 4.4 12.5 + - - +
157C LYS* 3.9 26.9 + - - -
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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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28A TYR* 3.8 24.9 - - - +
48A LYS* 4.8 5.2 - - + +
49A GLU* 1.3 74.5 - - - +
51A MET* 1.3 77.2 + - - +
52A VAL* 4.1 10.3 - - + -
56A LEU* 3.5 4.0 - - - +
57A VAL* 2.6 63.3 + - + +
59A MET* 4.3 12.8 - - + -
163A GLU* 5.3 3.1 - - - +
167A GLN* 4.4 13.2 - - - +
170A ALA* 4.5 7.2 - - + -
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Residues in contact with MET 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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50A VAL* 1.3 83.7 - - - +
52A VAL* 1.3 64.7 + - - +
53A ASP 4.2 1.0 + - - +
54A ASP* 4.2 7.6 - - - +
55A ARG* 3.2 40.2 - - - +
56A LEU* 3.3 32.5 - - + -
167A GLN* 4.5 7.4 - - - +
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Residues in contact with VAL 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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50A VAL* 4.1 5.6 - - + -
51A MET* 1.3 77.3 - - - +
53A ASP* 1.3 83.0 + - + +
54A ASP 3.4 2.0 - - - -
55A ARG* 2.8 23.8 + - - +
57A VAL* 3.7 27.8 - - + -
167A GLN* 4.5 4.5 - - + +
170A ALA* 3.7 26.7 - - + +
171A ARG* 3.7 42.8 - - + +
174A LEU* 4.5 9.4 - - + +
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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