Contacts of the strand formed by residues 38 - 46 (chain A) in PDB entry 2L03
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 ARG 38 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ASN* 5.5 5.4 - - + +
34A TYR* 3.8 6.2 + - + +
35A THR* 2.6 56.0 + - + +
36A PRO 3.6 0.2 - - - -
37A THR* 1.3 91.8 + - - +
39A MET* 1.3 63.6 + - - +
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Residues in contact with MET 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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10A ASN* 2.8 29.7 + - - +
11A GLY* 3.0 30.0 - - - +
12A ASP* 3.1 38.4 - - - +
32A THR 3.8 11.7 - - - +
33A TYR* 3.7 39.3 - - + +
34A TYR 4.6 4.3 - - - +
35A THR 5.1 0.4 - - - +
37A THR 5.9 0.4 - - - -
38A ARG* 1.3 77.5 - - - +
40A LYS* 1.3 68.0 + - - +
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Residues in contact with LYS 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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9A TYR 3.7 3.1 - - - -
10A ASN* 2.9 47.1 - - + +
11A GLY 4.3 2.2 - - - +
31A ARG* 3.6 1.2 - - - +
32A THR* 2.8 45.1 + - - +
33A TYR* 5.6 0.2 - - - -
34A TYR* 3.9 40.4 + - + -
38A ARG 5.8 0.2 - - - -
39A MET* 1.3 78.8 - - - +
41A VAL* 1.3 58.2 + - - +
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Residues in contact with VAL 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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8A ALA* 3.5 3.6 - - - +
9A TYR* 2.9 43.6 + - + +
11A GLY 4.4 1.3 - - - +
12A ASP 3.8 15.9 - - - +
13A ASN* 3.7 23.6 - - + +
14A CYS* 3.9 9.2 - - - +
29A THR* 4.3 9.4 - - + -
30A THR 3.6 9.2 - - - +
31A ARG* 4.4 11.2 - - + +
40A LYS* 1.3 76.8 - - - +
42A SER* 1.3 67.7 + - - +
43A LYS* 3.7 25.8 - - - -
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Residues in contact with SER 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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7A CYS 3.7 5.8 - - - -
8A ALA* 4.3 9.4 - - - -
28A MET* 4.0 4.1 - - - +
29A THR* 3.3 2.8 - - - +
30A THR* 2.7 59.1 + - - +
32A THR* 5.1 1.4 + - - -
41A VAL* 1.3 79.1 - - - +
43A LYS* 1.3 61.9 + - - +
44A SER* 5.5 0.2 - - - -
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Residues in contact with LYS 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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5A HIS* 2.8 22.9 - - + +
6A VAL* 3.3 1.4 - - - +
7A CYS 2.8 33.4 + - - +
13A ASN* 4.1 20.6 - - - +
14A CYS* 4.2 24.7 - - - +
28A MET 3.2 4.5 - - - +
29A THR* 3.1 31.3 + - + +
31A ARG* 5.6 4.2 - - - +
41A VAL* 3.7 20.8 - - + +
42A SER* 1.3 79.0 - - - +
44A SER* 1.3 66.5 + - - +
73A ASN* 2.8 38.4 + - - +
74A GLY 4.9 2.0 + - - -
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Residues in contact with SER 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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4A CYS* 4.8 1.1 - - - +
5A HIS 3.7 2.0 + - - +
6A VAL* 3.8 23.6 - - - -
27A CYS* 4.0 3.6 - - - +
28A MET* 3.1 40.2 + - - +
42A SER 5.5 0.2 - - - -
43A LYS* 1.3 77.6 - - - +
45A CYS* 1.3 66.2 + - - +
46A VAL* 4.4 10.7 - - - +
73A ASN* 4.9 0.3 + - - -
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Residues in contact with CYS 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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4A CYS* 3.8 20.4 - - - -
6A VAL* 3.8 16.0 - - + +
18A MET* 4.2 2.2 - - - -
20A CYS* 1.9 56.5 - - + -
21A PRO* 4.7 4.3 - - + -
24A VAL* 3.5 17.0 - - + +
26A TYR 3.9 2.7 - - - -
44A SER* 1.3 74.2 - - - +
46A VAL* 1.3 66.9 + - - +
47A PRO* 4.7 0.3 - - - +
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Residues in contact with VAL 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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24A VAL* 3.1 10.4 - - - +
26A TYR* 2.8 28.2 + - + +
27A CYS 4.7 0.2 - - - -
28A MET* 3.5 43.5 - - + +
44A SER* 4.4 9.2 - - - +
45A CYS* 1.3 78.4 - - - +
47A PRO* 1.3 73.4 - - + +
48A ARG 3.9 9.6 - - - +
49A CYS* 3.8 20.2 - - + -
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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