Contacts of the strand formed by residues 53 - 58 (chain A) in PDB entry 1K3X
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 ALA 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A THR* 3.3 6.6 - - - -
50A ARG 2.9 37.9 + - - +
52A LYS* 1.3 78.4 - - - +
54A LEU* 1.3 60.7 + - - +
55A LEU* 4.8 2.5 - - + +
65A TYR* 3.7 29.2 - - + +
66A SER 3.8 4.5 - - - -
67A HIS* 4.1 5.2 - - - -
121A PHE* 3.7 18.3 - - + -
122A LEU* 4.2 10.3 - - + -
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Residues in contact with LEU 54 (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 ILE* 4.1 23.3 - - + +
9A ALA* 4.9 2.0 - - + -
10A ALA* 4.0 23.8 - - + +
13A LEU* 4.0 11.0 - - + -
47A VAL* 3.6 17.5 - - + -
48A GLU 3.7 2.5 - - - -
49A THR* 4.2 3.1 - - + -
52A LYS 3.7 1.1 + - - +
53A ALA* 1.3 74.3 - - - +
55A LEU* 1.3 59.2 + - - +
56A THR* 3.4 26.0 - - - +
64A LEU 3.4 3.3 - - - +
65A TYR* 3.5 2.9 - - - -
66A SER* 2.9 53.2 + - - +
68A ASN* 5.9 0.7 - - - +
74A TRP* 3.9 26.0 - - + +
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Residues in contact with LEU 55 (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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47A VAL* 3.4 2.0 - - - -
48A GLU* 2.8 55.2 + - + +
50A ARG* 3.5 43.5 - - + +
53A ALA 4.8 2.2 - - - +
54A LEU* 1.3 76.4 - - - +
56A THR* 1.3 61.0 - - - +
57A HIS* 3.4 13.1 + - - +
63A THR* 3.7 19.5 - - + -
64A LEU 3.4 2.5 - - - -
65A TYR* 3.6 36.3 - - + -
111A LEU* 4.2 2.7 - - + -
116A LEU* 4.5 4.0 - - + -
122A LEU* 4.0 17.7 - - + -
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Residues in contact with THR 56 (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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13A LEU* 5.0 1.7 - - - +
44A VAL* 3.7 34.8 - - + -
46A HIS 4.0 2.5 - - - -
47A VAL* 4.1 9.0 - - + +
54A LEU* 3.4 22.0 - - - +
55A LEU* 1.3 68.3 - - - +
57A HIS* 1.3 62.3 + - - +
58A PHE* 3.5 15.8 - - + -
63A THR* 3.3 2.1 - - - -
64A LEU* 2.8 50.3 + - - +
74A TRP* 4.6 9.4 - - - -
93A LEU* 4.1 10.3 - - + -
100A ILE* 5.4 3.1 - - + -
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Residues in contact with HIS 57 (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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44A VAL* 3.3 6.8 - - - +
45A THR* 2.8 38.8 + - - +
46A HIS* 3.0 43.4 + + + +
48A GLU* 2.8 35.1 + - + +
50A ARG* 5.1 0.2 - - - -
55A LEU* 3.5 22.7 - - + +
56A THR* 1.3 74.0 - - - +
58A PHE* 1.3 61.8 + - - +
62A LEU 3.9 3.4 - - - +
63A THR* 2.9 29.6 + - + -
116A LEU* 4.0 21.0 - - + +
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Residues in contact with PHE 58 (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 LEU* 4.1 17.9 - - + -
27A PHE* 5.3 0.7 - + - -
39A LEU* 3.6 38.4 - - + -
42A GLN* 5.1 0.9 - - + -
43A HIS 3.3 7.6 - - - +
44A VAL* 3.8 28.7 - - + -
45A THR* 4.0 8.6 + - - +
56A THR* 3.5 24.9 - - + -
57A HIS* 1.3 75.9 - - - +
59A SER* 1.3 59.4 + - - +
60A ASN* 3.1 23.8 + - - +
61A ASP* 3.3 11.4 + - - +
62A LEU* 2.9 25.9 + - + +
64A LEU* 3.7 21.5 - - + -
93A LEU* 4.1 19.5 - - + -
110A MET* 4.0 5.4 - - + -
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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