Contacts of the strand formed by residues 25 - 36 (chain A) in PDB entry 1LKA
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 SER 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ARG* 3.4 15.8 - - - +
22A SER* 2.8 41.9 + - - -
24A SER* 1.3 82.2 - - - +
26A TRP* 1.3 67.7 + - - +
27A ALA* 5.5 0.2 - - - +
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Residues in contact with TRP 26 (chain A).
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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19A GLN* 3.5 10.6 - - + +
20A TYR 3.4 8.5 - - - -
21A ARG* 3.4 66.3 - - - +
22A SER* 4.0 1.6 - - - -
25A SER* 1.3 81.8 + - - +
27A ALA* 1.3 59.5 - - - +
52A THR* 3.8 31.4 - - + -
53A PHE 4.1 0.9 - - - -
54A ARG* 3.3 81.0 - - + +
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Residues in contact with ALA 27 (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 GLN* 3.8 4.9 - - - -
20A TYR* 2.9 58.3 + - + +
22A SER* 3.9 13.9 - - - +
25A SER* 5.5 0.2 - - - +
26A TRP* 1.3 75.3 - - - +
28A HIS* 1.3 66.3 + - - +
29A THR 3.4 0.3 + - - -
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Residues in contact with HIS 28 (chain A).
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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17A SER* 2.8 23.6 + - - +
18A LEU 3.8 3.8 - - - -
19A GLN* 3.9 11.1 - - - +
20A TYR* 4.6 1.7 - - - -
26A TRP 4.4 0.2 + - - -
27A ALA* 1.3 78.0 - - - +
29A THR* 1.3 63.9 + - - +
30A CYS 3.1 27.3 + - - -
31A GLY* 4.2 1.6 - - - -
62A LEU* 3.7 25.4 - - + +
132A TRP* 3.7 35.3 - + + +
141A LEU* 3.9 37.5 - - + +
186A GLY 2.9 24.9 + - - -
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Residues in contact with THR 29 (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 LEU* 2.8 23.6 + - + +
19A GLN* 4.6 0.4 - - - -
20A TYR* 3.7 27.5 - - + -
27A ALA 3.4 0.2 + - - -
28A HIS* 1.3 81.8 - - - +
30A CYS* 1.3 81.7 + - + +
46A CYS 4.8 3.0 + - - +
49A ARG* 3.3 21.2 + - - +
53A PHE* 4.4 18.6 - - + -
141A LEU* 6.2 0.2 - - - -
186A GLY* 3.6 15.9 - - - -
501A ACT 3.6 12.8 - - - +
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Residues in contact with CYS 30 (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 LEU* 2.8 35.4 + - + -
28A HIS* 3.1 14.6 + - - -
29A THR* 1.3 91.8 - - + +
31A GLY* 1.3 67.3 + - - +
46A CYS* 2.0 55.9 - - + -
186A GLY 3.7 6.1 - - - -
188A SER* 3.1 14.4 - - - +
501A ACT 4.0 7.4 - - - -
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Residues in contact with GLY 31 (chain A).
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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15A GLN* 3.6 12.3 - - - -
16A ILE* 3.4 15.7 - - - -
18A LEU* 4.4 1.8 - - - +
28A HIS* 4.5 3.1 - - - -
30A CYS* 1.3 78.1 - - - +
32A GLY* 1.3 52.4 + - - -
42A THR* 2.8 26.5 + - - -
131A GLY* 6.3 0.7 - - - -
186A GLY 3.9 5.6 + - - -
187A ASP* 4.1 2.4 + - - -
188A SER 2.8 11.6 + - - +
189A GLY* 3.2 5.5 - - - -
190A GLY* 3.6 11.0 - - - +
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Residues in contact with GLY 32 (chain A).
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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15A GLN* 3.7 8.8 + - - -
16A ILE* 3.0 41.8 + - - -
31A GLY* 1.3 74.7 - - - -
33A THR* 1.3 63.7 + - - -
40A VAL* 4.1 2.9 - - - -
41A MET 3.3 7.9 - - - -
42A THR* 4.3 0.7 - - - -
189A GLY 3.3 13.6 + - - -
190A GLY* 3.7 2.7 - - - -
191A PRO* 3.9 1.9 - - - +
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Residues in contact with THR 33 (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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14A SER* 3.4 21.3 + - - +
32A GLY* 1.3 74.8 - - - -
34A LEU* 1.3 73.3 + - - +
35A ILE* 3.3 10.5 + - + +
40A VAL* 3.4 4.6 - - - +
41A MET* 2.8 53.2 + - + +
112A GLY* 3.9 11.0 - - - -
114A LEU* 5.1 0.2 - - + -
189A GLY 5.0 0.2 + - - -
190A GLY 4.5 1.4 - - - -
191A PRO* 3.5 28.4 - - - +
202A VAL* 3.8 16.5 - - + +
205A VAL* 6.0 0.5 - - - +
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Residues in contact with LEU 34 (chain A).
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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13A PRO 5.3 1.1 - - - +
14A SER* 2.9 17.4 + - - +
16A ILE* 4.0 8.7 - - + +
33A THR* 1.3 70.4 - - - +
35A ILE* 1.3 53.0 + - - +
36A ARG 3.2 22.7 - - - +
39A TRP 3.7 7.9 - - - +
40A VAL* 4.0 15.7 - - + -
57A VAL* 4.3 9.2 - - + -
99A LEU* 4.2 14.6 - - + -
103A VAL* 3.8 28.0 - - + -
105A LEU* 4.3 1.3 - - + -
109A VAL* 3.8 15.9 - - + -
110A GLN 3.7 19.5 - - - +
111A LEU* 3.5 13.3 - - + -
112A GLY* 2.7 33.8 + - - -
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Residues in contact with ILE 35 (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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33A THR* 3.3 21.1 + - + +
34A LEU* 1.3 78.2 - - - +
36A ARG* 1.3 83.3 + - - +
39A TRP* 2.9 23.8 + - + +
41A MET* 4.1 16.6 - - + +
96A LEU* 3.9 17.5 - - + -
111A LEU* 3.9 16.4 - - - +
112A GLY 4.5 8.1 - - - +
114A LEU* 4.1 25.8 - - + -
233A ILE* 3.7 30.1 - - + -
237A ILE* 3.9 14.4 - - + -
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Residues in contact with ARG 36 (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* 3.2 15.4 - - - +
35A ILE* 1.3 98.9 + - - +
37A GLN* 1.4 67.2 + - - +
38A ASN* 3.0 5.8 + - - +
39A TRP* 3.2 41.8 + - + +
111A LEU* 3.4 15.7 - - - -
114A LEU* 5.7 3.6 - - - +
233A ILE* 5.0 2.8 - - - +
234A ASN* 3.6 21.6 + - - +
237A ILE* 3.6 37.3 - - + +
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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