Contacts of the strand formed by residues 13 - 19 (chain A) in PDB entry 1K3B
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 GLY 13 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A LEU 3.4 1.6 + - - -
12A LEU* 1.3 76.2 - - - +
14A THR* 1.3 62.0 + - - -
15A TRP* 4.0 5.7 + - - -
42A VAL 3.8 1.0 - - - +
43A TYR* 3.5 2.9 - - - -
44A LEU* 2.9 38.8 + - - +
117A LYS* 4.4 0.7 - - - -
119A GLY 3.5 10.3 - - - -
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Residues in contact with THR 14 (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 GLY* 1.3 72.2 - - - -
15A TRP* 1.3 64.3 + - - +
41A VAL* 3.6 16.2 - - + -
42A VAL 3.5 2.7 - - - +
43A TYR* 3.2 38.8 - - + -
117A LYS* 3.4 8.0 - - - +
118A VAL* 2.8 48.8 + - + -
119A GLY 3.0 15.2 + - - +
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Residues in contact with TRP 15 (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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10A ASP 4.0 12.6 - - - -
11A LEU* 3.0 44.0 + - + +
13A GLY 4.0 5.8 - - - -
14A THR* 1.3 79.4 - - - +
16A VAL* 1.3 61.9 + - - +
17A PHE* 3.7 26.5 - + + -
40A VAL 4.0 0.3 - - - +
41A VAL* 3.5 6.2 - - - +
42A VAL* 2.9 40.3 + - + +
44A LEU* 3.9 16.8 - - + -
68A PHE* 4.9 2.5 - + - -
81A PHE* 4.1 11.9 - + - -
94A CYS 3.5 25.8 - - - -
95A ASN* 3.6 23.6 - - - -
96A GLU 4.0 1.1 - - - -
97A THR* 3.8 19.3 - - + -
115A GLY 3.9 5.2 - - - -
116A LYS 3.5 11.4 - - - -
117A LYS* 3.5 23.7 - - + +
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Residues in contact with VAL 16 (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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15A TRP* 1.3 77.2 - - - +
17A PHE* 1.3 62.8 + - - +
18A GLN* 3.8 19.7 + - + +
39A LYS* 3.6 32.1 - - + -
40A VAL 3.8 2.5 - - - -
41A VAL* 4.1 15.5 - - + +
114A THR 3.7 1.0 - - - +
115A GLY* 3.3 2.9 - - - -
116A LYS* 2.9 37.4 + - + +
118A VAL* 3.5 32.5 - - + -
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Residues in contact with PHE 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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15A TRP* 3.7 20.9 - + + -
16A VAL* 1.3 75.8 - - - +
18A GLN* 1.3 61.8 + - - +
19A VAL* 3.8 2.1 + - - +
38A LYS 3.7 0.3 - - - +
39A LYS* 3.3 4.3 - - - +
40A VAL 2.9 39.7 + - - +
42A VAL* 3.4 35.2 - - + -
68A PHE* 3.8 20.0 - + - -
70A ILE* 3.8 24.9 - - + -
77A TRP* 3.4 50.7 - + + -
113A PHE* 3.8 18.2 - + + -
114A THR 3.5 2.5 - - - -
115A GLY* 3.5 22.2 - - - -
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Residues in contact with GLN 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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16A VAL* 3.8 23.2 - - + +
17A PHE* 1.3 71.9 - - - +
19A VAL* 1.3 60.2 + - - +
36A GLN* 3.3 37.7 + - + +
38A LYS 3.4 10.6 + - - +
39A LYS* 3.9 21.6 - - - +
113A PHE* 3.1 4.7 - - - -
114A THR* 2.9 36.3 + - - +
116A LYS* 6.1 4.5 - - + -
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Residues in contact with VAL 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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17A PHE 4.0 6.1 - - - +
18A GLN* 1.3 75.6 - - - +
20A GLY* 1.3 68.7 + - - +
36A GLN* 4.1 2.4 - - - +
37A GLU* 2.8 22.5 + - - -
38A LYS* 2.7 53.7 + - + +
40A VAL* 4.5 4.7 - - + -
77A TRP* 3.7 36.3 - - + -
102A VAL* 4.2 7.0 - - + -
111A ALA* 3.7 18.8 - - + -
112A CYS 3.5 4.9 - - - +
113A PHE* 4.0 2.5 - - + -
503A SO4 4.5 1.1 - - - +
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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