Contacts of the strand formed by residues 16 - 27 (chain A) in PDB entry 1LKF
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 VAL 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A LYS* 4.1 0.5 - - - +
12A VAL* 3.0 48.7 + - + +
13A ASP* 3.5 8.8 + - - +
14A ASP 5.1 0.4 - - - -
15A LYS* 1.3 77.1 + - - +
17A THR* 1.3 68.8 + - - +
18A LEU* 3.9 17.7 - - + -
41A ILE* 4.1 6.1 - - + -
42A LYS 3.1 5.2 - - - +
43A ASP* 3.4 35.4 - - + +
116A TYR* 4.6 2.9 - - + -
118A PHE* 3.7 24.7 - - + -
137A ALA* 4.1 12.6 - - + -
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Residues in contact with THR 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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9A VAL* 4.9 4.3 - - + -
10A LYS 3.5 15.0 - - - +
11A LYS* 4.0 22.7 - - + +
14A ASP 6.0 0.7 - - - -
15A LYS 5.3 1.2 + - - -
16A VAL* 1.3 77.2 + - - +
18A LEU* 1.3 66.2 + - - +
19A TYR* 3.5 42.1 + - + +
40A PHE 3.6 1.4 - - - +
41A ILE* 3.9 1.0 - - - -
42A LYS* 3.0 32.9 + - - +
44A LYS* 5.6 5.2 - - - -
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Residues in contact with LEU 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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8A SER 3.9 0.2 - - - +
9A VAL* 3.4 3.5 - - - -
10A LYS* 2.7 58.8 + - + +
12A VAL* 3.6 17.0 - - + -
16A VAL* 3.9 17.0 - - + -
17A THR* 1.3 73.5 - - - +
19A TYR* 1.3 62.5 - - - +
20A LYS* 6.4 0.2 - - + -
39A ASN* 6.3 2.2 - - + -
40A PHE 3.4 2.5 - - - +
41A ILE* 3.9 28.9 - - + -
137A ALA 3.6 17.3 - - - +
138A PHE* 3.9 32.3 - - + -
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Residues in contact with TYR 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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7A VAL* 3.9 6.3 - - + -
8A SER 3.3 3.4 - - - -
9A VAL* 3.7 29.4 - - + -
17A THR* 3.5 40.2 + - + +
18A LEU* 1.3 74.7 - - - +
20A LYS* 1.3 60.4 + - - +
38A PHE 3.4 1.0 - - - +
39A ASN* 3.4 4.6 - - - -
40A PHE* 2.7 44.2 + - + +
42A LYS* 3.6 21.1 - - + +
285A HIS* 3.5 61.8 + + + -
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Residues in contact with LYS 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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6A PRO 3.7 1.6 - - - +
7A VAL* 3.2 8.3 - - - +
8A SER* 2.9 51.2 + - - +
19A TYR* 1.3 76.1 - - - +
21A THR* 1.3 67.7 + - - +
22A THR* 4.7 4.0 - - - +
37A THR* 3.9 26.1 - - + +
38A PHE 3.3 3.4 - - - +
39A ASN* 3.1 26.2 - - - +
138A PHE* 5.8 0.6 - - - -
140A GLU* 4.8 10.3 + - - -
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Residues in contact with THR 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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4A ILE* 3.6 12.1 - - - +
5A THR* 3.0 28.7 + - - -
6A PRO 4.4 0.7 - - - -
7A VAL* 4.3 12.7 - - - +
20A LYS* 1.3 81.1 - - - +
22A THR* 1.3 61.8 + - - +
23A ALA 4.2 0.2 - - - -
36A LEU 3.7 1.0 - - - +
37A THR* 3.7 0.2 - - - -
38A PHE* 2.9 47.3 + - + +
40A PHE* 4.2 4.9 - - + -
285A HIS 4.0 15.5 - - - +
286A LYS* 5.4 0.3 - - - -
287A VAL* 4.3 19.3 + - + +
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Residues in contact with THR 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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3A LYS 3.8 1.4 - - - +
4A ILE* 3.4 2.4 - - - -
5A THR* 2.9 48.6 + - + +
20A LYS* 4.7 4.9 - - - +
21A THR* 1.3 76.3 + - - +
23A ALA* 1.3 65.6 + - - +
24A THR* 4.8 3.6 - - - +
35A ILE* 3.8 23.1 - - + -
36A LEU 3.3 10.1 - - - +
37A THR* 3.4 26.1 + - - +
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Residues in contact with ALA 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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3A LYS 3.4 4.9 - - - -
4A ILE* 4.0 10.5 - - + +
21A THR 4.2 0.2 + - - -
22A THR* 1.3 75.9 - - - +
24A THR* 1.3 63.8 + - - +
25A ALA 4.3 0.2 - - - -
34A GLN 3.8 0.5 - - - +
35A ILE* 3.6 0.9 - - - -
36A LEU* 2.8 38.9 + - + +
38A PHE* 4.3 5.6 - - + -
278A TYR* 3.5 35.4 - - + +
287A VAL* 4.2 11.9 - - + -
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Residues in contact with THR 24 (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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2A GLY* 3.1 26.7 + - - -
3A LYS* 2.9 25.6 + - + +
22A THR* 4.8 3.3 - - - +
23A ALA* 1.3 76.9 + - - +
25A ALA* 1.3 63.4 + - - +
26A ASP* 3.4 27.8 - - - +
33A SER* 5.4 0.4 - - - +
34A GLN 3.3 8.9 + - - +
35A ILE* 4.2 18.5 - - + +
278A TYR* 4.1 3.6 + - - -
289A LEU* 5.8 1.4 - - - +
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Residues in contact with ALA 25 (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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1A GLU 4.0 10.3 - - - +
23A ALA 4.3 0.2 - - - -
24A THR* 1.3 73.9 - - - +
26A ASP* 1.3 60.8 + - - +
34A GLN* 2.9 34.4 + - - +
36A LEU* 6.2 0.2 - - - +
274A PHE* 3.3 26.4 - - + -
276A SER* 4.1 14.6 - - - -
278A TYR* 3.6 16.7 + - - +
289A LEU* 5.0 3.1 - - + -
292A THR* 4.4 6.3 - - + -
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Residues in contact with ASP 26 (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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1A GLU* 3.2 44.5 + - + +
2A GLY* 4.7 0.5 - - - -
24A THR* 3.4 20.6 - - - +
25A ALA* 1.3 75.2 - - - +
27A SER* 1.3 64.0 + - - +
28A ASP* 3.9 12.3 + - - +
32A ILE 3.6 5.4 - - - +
33A SER* 3.2 31.2 + - - -
274A PHE* 3.5 10.5 - - - -
294A GLU* 4.8 0.7 - - - +
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Residues in contact with SER 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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26A ASP* 1.3 73.8 - - - +
28A ASP* 1.3 62.1 + - - +
30A PHE* 3.0 31.6 + - - +
31A LYS* 3.0 15.6 + - - -
32A ILE 2.9 20.0 + - - +
274A PHE* 3.7 23.3 - - - -
294A GLU* 2.8 28.7 + - - -
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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