Contacts of the strand formed by residues 16 - 23 (chain A) in PDB entry 1LFD
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 CYS 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A GLY 3.6 15.0 - - - -
15A ASP* 1.3 75.8 - - - +
17A CYS* 1.3 64.9 + - - +
35A LEU* 4.1 16.2 - - + -
36A VAL 3.1 17.7 - - - +
37A THR* 3.5 14.8 - - + +
84A PHE* 3.8 7.5 - - - -
15C ASP* 3.9 4.2 - - - +
16C CYS* 2.8 36.5 + - - +
18C ILE* 4.2 6.5 - - - -
35C LEU* 3.6 29.6 - - - -
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Residues in contact with CYS 17 (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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16A CYS* 1.3 74.4 - - - +
18A ILE* 1.3 65.0 + - - +
19A ILE* 3.6 9.5 + - - -
35A LEU* 3.6 5.2 - - - -
36A VAL* 2.9 41.9 + - - +
84A PHE* 4.5 11.2 - - + -
87A MET* 3.9 28.7 - - - -
93A TYR* 3.7 23.8 - - + +
14C GLY 3.2 14.8 - - - +
15C ASP* 4.6 5.6 - - - +
16C CYS* 4.7 0.7 - - - +
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Residues in contact with ILE 18 (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 CYS* 1.3 69.6 - - - +
19A ILE* 1.3 62.4 + - - +
20A ARG* 5.6 2.6 - - + +
33A SER* 4.0 15.9 - - - +
34A ILE 3.6 5.6 - - - +
35A LEU* 3.7 19.1 - - + -
93A TYR* 3.4 19.6 - - - +
236B ILE* 3.7 33.4 - - + -
264B TYR* 4.1 15.0 - - + -
267B MET* 4.4 20.2 - - + -
14C GLY* 3.0 22.4 + - - +
16C CYS* 3.9 21.3 - - - -
37C THR* 5.3 4.5 - - + -
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Residues in contact with ILE 19 (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 CYS* 3.6 17.2 + - - -
18A ILE* 1.3 79.5 - - - +
20A ARG* 1.3 63.6 + - - +
21A VAL* 3.8 17.2 + - + -
33A SER* 3.2 4.8 - - - -
34A ILE* 3.0 51.6 + - + +
36A VAL* 3.4 33.0 - - + -
45A VAL* 4.3 8.1 - - + -
65A LEU* 5.7 0.2 - - + -
83A VAL* 5.4 0.9 - - + -
87A MET* 4.0 3.6 - - + -
93A TYR* 3.6 15.7 - - + +
95A PHE* 3.7 38.4 - - + -
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Residues in contact with ARG 20 (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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18A ILE* 5.6 2.9 - - + +
19A ILE* 1.3 72.5 - - - +
21A VAL* 1.3 57.7 + - - +
22A SER 4.2 0.2 - - - -
31A TYR* 3.6 53.0 + - + -
32A LYS 4.1 3.6 - - - -
33A SER* 3.9 9.9 - - - +
93A TYR* 2.8 13.9 + - + +
94A ASP* 3.5 23.0 + - + +
95A PHE* 2.7 34.8 + - - +
237B GLU* 3.4 20.0 + - - -
267B MET* 6.2 0.2 - - - +
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Residues in contact with VAL 21 (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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19A ILE* 3.8 24.5 - - + -
20A ARG* 1.3 76.4 - - - +
22A SER* 1.3 62.9 + - - +
31A TYR* 3.3 1.7 - - - -
32A LYS 2.9 38.2 + - - +
34A ILE* 3.8 23.3 - - + -
49A ALA* 4.0 14.1 - - + -
53A HIS* 3.0 23.0 - - + -
65A LEU* 5.1 5.6 - - + -
95A PHE* 3.4 10.3 - - + +
96A ILE 4.7 0.4 - - - -
97A LEU* 3.8 31.0 - - + +
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Residues in contact with SER 22 (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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20A ARG 4.2 0.2 + - - -
21A VAL* 1.3 77.5 - - - +
23A LEU* 1.3 65.4 + - - +
30A MET 3.2 25.4 - - - -
31A TYR* 4.2 4.3 - - - +
53A HIS* 4.4 2.7 - - - -
68A ILE* 4.5 8.1 - - - +
95A PHE 2.8 16.8 + - - -
96A ILE* 3.3 13.9 - - - +
97A LEU* 2.8 26.3 + - - -
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Residues in contact with LEU 23 (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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22A SER* 1.3 78.8 + - - +
24A ASP* 1.3 63.3 + - - +
25A VAL* 3.0 49.3 + - + +
27A ASN* 4.5 8.5 - - - +
29A ASN* 5.2 5.5 + - - +
53A HIS* 4.1 36.7 + - + +
55A LEU* 4.0 22.4 - - + -
63A TYR* 4.8 3.1 - - + -
96A ILE* 4.6 3.4 - - - +
97A LEU* 3.4 41.5 - - + +
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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