Contacts of the strand formed by residues 44 - 52 (chain A) in PDB entry 2L33
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 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A THR 3.8 4.3 - - - +
39A GLY* 3.5 28.6 - - - -
40A GLY 5.0 4.7 + - - -
42A HIS 5.8 0.4 - - - +
43A ASP* 1.3 86.6 + - - +
45A ARG* 1.3 78.8 + - - +
46A PHE* 3.7 13.5 - - + -
62A SER* 3.0 43.1 + - - +
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Residues in contact with ARG 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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36A SER* 4.2 4.8 + - - +
37A GLU* 3.8 3.1 + - - -
38A THR* 3.1 48.9 + - + +
43A ASP* 2.7 33.4 + - - +
44A LYS* 1.3 81.5 + - - +
46A PHE* 1.3 64.6 + - - +
47A VAL* 5.3 5.6 - - + -
60A ALA* 4.8 16.4 - - - +
61A GLY 3.9 6.7 + - - -
62A SER* 5.7 1.0 + - - -
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Residues in contact with PHE 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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34A LEU* 4.6 3.4 - - + -
36A SER 3.3 6.1 - - - +
37A GLU* 3.2 43.1 - - + -
38A THR 3.5 18.8 - - - -
44A LYS* 3.7 23.6 - - + -
45A ARG* 1.3 79.5 - - - +
47A VAL* 1.3 64.7 + - - +
60A ALA* 3.1 5.5 - - - +
61A GLY 2.8 37.7 + - - +
62A SER 3.8 6.7 - - - -
63A ASN* 3.6 27.6 - - + +
64A LYS* 3.6 26.7 - - + +
67A ALA* 3.4 3.9 - - + +
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Residues in contact with VAL 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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34A LEU* 3.6 3.7 - - - +
35A ILE* 2.8 38.8 + - + +
36A SER* 2.8 35.0 + - - +
45A ARG* 5.3 6.3 - - + +
46A PHE* 1.3 79.5 - - - +
48A MET* 1.3 57.8 + - - +
58A GLN* 4.0 28.7 - - + +
59A GLY 3.2 14.6 - - - +
60A ALA* 3.8 15.7 - - + -
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Residues in contact with MET 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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32A TYR* 4.4 5.8 - - + +
33A GLU* 3.3 32.3 - - - +
34A LEU* 3.3 39.0 - - + +
35A ILE* 4.2 2.7 - - - -
47A VAL* 1.3 73.1 - - - +
49A GLU* 1.3 61.0 + - - +
58A GLN* 3.2 4.4 - - - -
59A GLY 2.9 30.8 + - - -
64A LYS* 3.3 38.4 - - + +
67A ALA* 3.5 10.5 - - + -
68A LYS* 3.7 38.4 - - + +
71A ALA* 3.5 4.9 - - + +
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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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31A LYS* 2.7 35.9 + - - +
32A TYR* 3.4 3.3 - - - -
33A GLU* 2.9 41.7 + - + +
35A ILE* 3.6 25.9 - - + +
48A MET* 1.3 74.1 - - - +
50A VAL* 1.3 64.2 + - - +
56A LYS* 3.6 31.2 - - + +
57A PHE 3.5 4.3 - - - +
58A GLN* 3.1 31.6 + - + -
71A ALA* 4.8 0.4 - - - -
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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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23A LEU* 3.7 18.6 - - + -
30A LEU* 4.9 1.1 - - + -
31A LYS 3.0 6.1 - - - +
32A TYR* 3.6 35.2 - - + -
48A MET 4.3 0.4 - - - -
49A GLU* 1.3 75.9 - - - +
51A GLU* 1.3 64.9 + - - +
52A VAL* 3.8 14.3 + - + -
55A GLN 3.3 2.1 - - - +
56A LYS* 3.2 3.4 - - - -
57A PHE* 2.8 50.6 + - + +
71A ALA* 3.3 34.3 - - + +
72A ALA* 4.1 2.0 - - - +
75A ALA* 4.6 0.7 - - + -
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Residues in contact with GLU 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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29A GLY 4.0 15.4 - - - +
30A LEU* 3.2 27.9 - - - +
31A LYS* 3.0 43.5 + - + +
50A VAL* 1.3 70.7 - - - +
52A VAL* 1.3 61.6 + - - +
53A ASP 4.4 0.2 + - - -
54A GLY* 3.9 19.9 - - - +
55A GLN 3.3 4.3 - - - -
56A LYS* 3.2 35.3 + - + +
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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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23A LEU* 3.5 37.5 - - + -
27A ARG* 3.7 24.2 - - + -
30A LEU* 3.8 4.5 - - + -
50A VAL* 3.8 11.0 - - + +
51A GLU* 1.3 76.8 - - - +
53A ASP* 1.3 72.6 + - - +
54A GLY 3.0 3.6 - - - -
55A GLN* 2.8 37.4 + - - +
57A PHE* 4.8 0.9 - - + -
75A ALA* 3.8 14.4 - - + -
79A LEU* 3.5 26.9 - - + +
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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