Contacts of the strand formed by residues 75 - 85 (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 TYR 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A ILE 3.6 0.7 - - - +
71A VAL* 3.4 4.5 - - - +
72A LEU 2.9 33.8 + - - +
73A ASN* 3.3 27.8 - - + -
74A ASP* 1.3 83.3 - - + +
76A LYS* 1.3 62.4 + - - +
77A TRP* 4.2 17.5 - + + +
102A VAL* 4.1 12.3 - - + -
103A HIS 3.5 7.0 - - - -
104A ASP* 3.4 35.2 + - + +
105A VAL* 4.0 0.4 - - - +
109A ASN* 4.6 6.7 + - + +
503A SO4 3.3 38.3 + - - -
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Residues in contact with LYS 76 (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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69A GLU* 4.2 5.1 + - - +
70A ILE 3.2 6.3 - - - +
71A VAL* 4.0 22.2 - - + +
75A TYR* 1.3 77.2 - - - +
77A TRP* 1.3 61.3 + - - +
101A TRP 3.8 1.9 - - - +
102A VAL* 3.3 4.7 - - - +
103A HIS* 2.9 40.1 + - - +
105A VAL* 3.9 35.7 - - + +
285B LYS* 4.1 16.1 + - - +
288B GLN* 2.8 32.7 + - - +
321B TYR* 3.4 27.5 + - - +
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Residues in contact with TRP 77 (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* 3.4 42.6 - + + -
19A VAL* 3.7 27.6 - - + -
40A VAL* 3.8 35.7 - - + -
42A VAL* 5.0 1.7 - - + +
68A PHE* 3.5 3.3 - - + +
69A GLU* 3.1 8.6 - - - +
70A ILE* 2.8 63.3 + - + +
72A LEU* 4.7 14.6 + - + +
75A TYR* 4.3 17.4 + + + +
76A LYS* 1.3 75.3 - - - +
78A PHE* 1.3 60.7 + - - +
101A TRP 3.8 3.8 - - - -
102A VAL* 3.5 33.1 - - + +
113A PHE* 3.8 20.9 - + + -
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Residues in contact with PHE 78 (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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63A ILE* 3.9 9.6 - - + -
68A PHE* 3.3 15.0 - - - +
69A GLU* 4.7 2.9 - - + -
77A TRP* 1.3 74.7 - - - +
79A ALA* 1.3 86.7 + - - +
80A PHE* 3.7 25.4 - + - -
100A GLY* 3.2 0.7 - - - -
101A TRP* 2.9 73.0 + + + +
113A PHE* 3.3 4.0 - - - -
270B TYR* 3.6 17.9 - + - -
281B LEU* 3.5 40.8 - - + -
285B LYS* 3.3 37.0 - - + +
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Residues in contact with ALA 79 (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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67A GLY* 3.2 2.8 - - - -
68A PHE* 3.2 36.2 + - + -
78A PHE* 1.3 92.6 - - - +
80A PHE* 1.3 60.5 + - - +
97A THR* 3.8 23.3 - - - +
98A MET 4.0 3.1 - - - +
99A THR 5.1 0.4 - - - -
100A GLY* 3.7 14.6 - - - -
101A TRP* 5.1 0.9 - - - -
113A PHE* 3.6 17.9 - - + -
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Residues in contact with PHE 80 (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 THR* 4.2 16.4 - - + -
66A GLN* 3.4 34.5 - - + +
78A PHE* 3.7 21.1 - + - -
79A ALA* 1.3 75.7 - - - +
81A PHE* 1.3 66.6 + - - +
97A THR* 3.4 5.1 - - - -
98A MET* 2.8 41.2 + - + +
99A THR 5.4 1.0 + - - -
101A TRP* 4.8 6.9 - + - -
269B GLN 3.8 19.1 - - - -
270B TYR 3.4 22.4 - - - -
272B GLN* 3.4 26.9 - - - -
278B PHE* 5.8 2.2 - + - -
281B LEU* 3.7 17.9 - - + -
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Residues in contact with PHE 81 (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 THR* 4.9 0.2 + - - -
4A ALA* 4.3 8.6 - - + +
6A CYS* 3.4 44.4 - - + -
7A THR 5.0 0.9 - - - -
11A LEU* 3.9 25.1 - - + -
15A TRP* 4.1 11.9 - + - -
62A ILE* 3.9 19.3 - - + -
65A ASN 3.9 2.0 - - - -
66A GLN 2.9 29.1 + - - +
67A GLY* 3.6 19.7 - - - -
68A PHE* 3.8 22.4 - + - -
80A PHE* 1.3 77.7 - - - +
82A LYS* 1.3 64.1 + - - +
83A TYR* 3.7 9.9 - - - -
93A TYR 4.1 1.8 - - - +
94A CYS* 3.8 23.6 - - - -
96A GLU 3.6 10.3 - - - +
97A THR* 4.3 0.2 - - - +
98A MET* 3.6 7.6 - - - +
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Residues in contact with LYS 82 (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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80A PHE 3.6 1.4 + - - -
81A PHE* 1.3 75.1 - - - +
83A TYR* 1.3 64.7 + - - +
84A LYS* 3.7 38.2 - - - +
92A THR* 3.4 5.4 - - - +
93A TYR* 2.7 47.0 + - + +
96A GLU* 3.0 52.8 + - + +
97A THR* 3.7 12.3 - - - +
98A MET* 3.7 18.6 - - - +
116A LYS* 6.0 1.1 - - - +
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Residues in contact with TYR 83 (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 THR* 3.5 35.1 - - + +
3A PRO* 3.7 26.0 - - + +
4A ALA* 4.9 2.7 - - + +
81A PHE 3.7 12.3 - - - -
82A LYS* 1.3 78.5 - - - +
84A LYS* 1.3 67.4 + - - +
85A GLU* 3.5 30.6 + - + -
90A VAL* 4.5 6.3 - - + -
91A THR 2.9 13.0 - - - +
92A THR* 4.2 11.7 - - - +
93A TYR* 4.6 0.7 - - - -
98A MET* 3.6 41.8 - - + +
272B GLN* 5.6 2.8 - - - +
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Residues in contact with LYS 84 (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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82A LYS* 3.7 31.7 - - - +
83A TYR* 1.3 78.3 - - - +
85A GLU* 1.3 64.5 + - - +
86A GLU* 3.7 3.2 + - + +
89A LYS* 3.3 6.6 - - - +
90A VAL* 3.4 2.4 - - - -
91A THR* 2.8 37.1 + - - +
93A TYR* 4.2 21.1 + - + +
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Residues in contact with GLU 85 (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 PRO* 4.5 7.4 - - - +
83A TYR* 3.5 29.2 + - + -
84A LYS* 1.3 74.7 - - - +
86A GLU* 1.3 57.0 + - - +
87A GLY* 3.2 10.0 + - - +
88A SER 5.7 1.6 - - - +
89A LYS 3.5 4.9 - - - -
90A VAL* 4.2 18.6 - - + -
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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