Contacts of the strand formed by residues 63 - 67 (chain D) in PDB entry 1KLG
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 LYS 63 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D VAL* 4.3 14.6 - - - +
42D ASP* 5.3 2.0 + - - +
50D ILE* 4.3 12.9 - - + +
51D TYR 3.5 3.1 - - - +
52D ASN* 3.5 25.4 + - - +
61D TYR* 3.7 1.6 - - - -
62D ASP* 1.3 93.3 + - - +
64D VAL* 1.3 66.5 + - - +
95D PHE* 4.0 9.0 - - + -
97D SER* 3.1 29.1 + - - +
98D LYS* 4.2 21.5 - - - +
107D GLY 3.3 7.2 + - - +
108D LYS* 3.6 19.5 - - + -
109D THR* 3.2 22.5 + - - +
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Residues in contact with VAL 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D VAL* 4.4 7.4 - - + -
49D LEU 3.7 1.2 - - - +
50D ILE* 3.3 4.4 - - - +
51D TYR* 2.8 41.8 + - + +
53D ILE* 4.1 29.6 - - + +
61D TYR* 3.7 19.1 - - + -
63D LYS* 1.3 76.7 - - - +
65D LYS* 1.3 67.9 + - - +
66D THR* 4.6 1.8 - - - +
84D VAL* 5.6 0.4 - - + -
109D THR* 3.2 32.5 - - + +
111D MET* 4.0 28.5 - - + -
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Residues in contact with LYS 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LYS* 4.7 2.6 - - - +
44D PHE* 4.3 6.8 - - + -
45D PHE* 6.1 0.8 - - - -
48D ASP* 3.7 37.6 + - + +
49D LEU 3.4 5.2 - - - +
50D ILE* 4.0 8.3 - - + +
64D VAL* 1.3 74.0 - - - +
66D THR* 1.3 62.5 + - - +
67D GLU* 3.0 33.8 + - - -
89D TYR* 4.8 0.2 + - - -
94D TYR 2.8 25.2 + - - +
95D PHE* 3.5 33.0 - - + +
109D THR 3.2 7.6 + - - +
110D CYS* 3.3 22.3 - - - +
111D MET* 3.0 25.3 + - - +
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Residues in contact with THR 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D ASP* 3.2 3.5 - - - +
49D LEU* 2.9 36.8 + - + +
51D TYR* 4.2 11.4 - - + -
64D VAL* 4.0 2.6 + - - -
65D LYS* 1.3 73.3 - - - +
67D GLU* 1.3 59.5 - - - +
68D LEU* 3.9 4.7 + - + +
84D VAL* 5.9 1.8 - - + -
111D MET* 3.3 19.3 - - - +
112D TYR 3.3 4.7 - - - -
113D GLY 2.6 33.6 + - - +
115D ILE* 3.8 29.2 - - + -
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Residues in contact with GLU 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A MET 4.7 0.7 - - - +
37A ALA 4.7 2.9 - - - +
39A LYS* 2.6 43.1 + - - -
45D PHE* 5.8 1.6 - - - -
47D TRP* 3.2 25.4 + - + +
48D ASP* 3.7 20.2 - - + +
65D LYS* 3.0 32.7 + - + -
66D THR* 1.3 73.2 - - - +
68D LEU* 1.3 61.3 + - - +
89D TYR* 3.6 4.9 + - - -
111D MET 2.8 11.7 + - - +
112D TYR* 3.2 23.7 - - + -
113D GLY 3.0 20.6 + - - -
218D ASN* 3.4 7.0 + - - +
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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