Contacts of the strand formed by residues 23 - 26 (chain A) in PDB entry 1LK7
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 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ASP 5.2 1.6 - - - +
22A MET* 1.3 74.4 - - - +
24A ILE* 1.3 61.0 + - - +
52A VAL* 3.3 18.4 - - + +
54A VAL* 3.5 27.8 - - + -
77A VAL* 4.1 20.9 - - + -
78A ASP 5.8 0.4 - - - +
79A ALA 3.3 27.4 - - - +
80A ILE* 3.8 7.7 - - + -
81A ASP* 2.8 40.4 + - - +
82A VAL 3.5 3.1 + - - +
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Residues in contact with ILE 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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18A ILE* 3.8 28.0 - - + -
22A MET* 3.5 44.9 - - + +
23A VAL* 1.3 76.9 - - - +
25A GLY* 1.3 73.4 + - - +
26A LEU* 3.4 16.7 + - + +
35A PHE* 4.7 4.7 - - + -
39A LEU* 5.1 6.7 - - + -
51A ILE* 5.1 7.9 - - + -
52A VAL 2.8 15.6 + - - +
53A GLY* 3.2 5.2 - - - -
54A VAL* 2.8 26.9 + - - -
80A ILE* 4.7 0.9 - - - -
82A VAL* 3.2 14.4 - - + +
84A VAL* 4.5 14.4 - - + -
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Residues in contact with GLY 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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24A ILE* 1.3 76.2 - - - +
26A LEU* 1.3 58.9 + - - +
27A GLY 3.9 0.4 - - - -
54A VAL* 3.4 11.4 - - - -
56A THR* 5.0 2.0 - - - -
80A ILE* 3.9 5.5 - - - +
82A VAL 2.9 13.0 + - - -
83A ALA* 3.5 7.1 - - - -
84A VAL* 3.1 26.1 + - - +
110A ILE* 3.9 22.7 - - - -
111A GLU* 6.1 0.4 - - - -
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Residues in contact with LEU 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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24A ILE* 3.6 27.8 - - + +
25A GLY* 1.3 74.9 - - - +
27A GLY* 1.3 57.3 + - - +
32A THR* 5.2 0.7 - - - -
35A PHE* 4.3 17.5 - - + -
36A ILE* 4.3 22.0 - - + -
39A LEU* 4.3 10.3 - - + -
53A GLY* 3.7 21.8 - - - -
54A VAL 2.8 12.9 + - - +
55A PRO* 4.1 7.9 - - + -
56A THR* 2.7 40.3 + - - +
60A ALA* 3.5 4.1 - - + +
64A ALA* 4.0 27.4 - - + -
69A ILE* 4.7 9.2 - - + -
71A ILE* 4.7 1.1 - - + -
84A VAL 4.2 0.7 - - - -
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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