Contacts of the strand formed by residues 98 - 105 (chain A) in PDB entry 3K3B
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 ASN 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A TYR* 1.3 77.3 - - - +
99A CYS* 1.3 53.6 + - - +
258A ILE 5.9 0.7 - - - +
260A LYS* 3.2 39.9 - - + +
262A ASN* 3.6 2.4 + - - -
322A ASP* 4.3 27.1 + - - +
323A SER* 2.5 39.9 + - - +
327A ARG 4.9 1.8 + - - -
328A THR* 2.4 28.8 + - - -
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Residues in contact with CYS 99 (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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89A ILE* 3.6 28.5 - - + -
92A GLU* 3.9 17.3 - - - -
93A VAL* 3.8 22.4 - - + -
97A TYR* 4.8 0.4 - - - -
98A ASN* 1.3 82.0 - - - +
100A THR* 1.3 67.3 + - - +
260A LYS 2.7 11.4 + - - +
261A LEU* 3.4 4.8 - - + -
262A ASN* 2.9 26.5 + - - -
323A SER* 4.3 0.2 - - - -
328A THR* 3.4 4.5 - - - -
329A ARG* 3.1 28.3 - - - +
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Residues in contact with THR 100 (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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89A ILE* 4.9 0.2 - - - +
99A CYS* 1.3 74.0 + - - +
101A ILE* 1.3 69.0 + - - +
102A PHE* 3.4 37.9 - - + -
262A ASN* 3.4 17.2 + - + +
264A VAL* 4.0 14.4 - - + -
320A LEU* 4.4 5.3 - - + +
323A SER* 3.1 34.8 + - - -
324A LEU* 4.3 7.7 - - - +
329A ARG 3.4 5.0 + - - +
330A THR* 3.3 7.6 - - - +
331A SER 3.1 22.7 + - - +
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Residues in contact with ILE 101 (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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85A VAL* 4.5 1.8 - - + -
86A VAL* 4.1 29.2 - - + -
89A ILE* 3.7 38.8 - - + -
100A THR* 1.3 77.7 - - - +
102A PHE* 1.3 66.6 + - - +
115A MET* 3.6 20.6 - - + +
135A ILE* 4.6 2.9 - - + -
261A LEU* 4.1 7.6 - - + -
262A ASN 2.9 7.5 + - - -
263A LEU* 3.5 24.6 - - + -
264A VAL* 2.8 28.2 + - - +
331A SER* 3.3 14.1 - - - +
333A ILE* 4.0 15.7 - - + -
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Residues in contact with PHE 102 (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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100A THR* 3.4 23.3 - - + -
101A ILE* 1.3 71.6 - - - +
103A ALA* 1.3 61.1 + - - +
115A MET* 3.4 12.8 - - - +
264A VAL* 3.4 24.2 - - + -
266A LEU* 4.0 11.0 - - + -
295A LEU* 3.5 42.0 - - + -
299A ILE* 4.4 4.7 - - + -
316A LEU* 4.9 0.7 - - + -
320A LEU* 3.6 25.8 - - + -
324A LEU* 4.2 10.5 - - + -
330A THR* 3.9 17.5 - - + -
331A SER 2.8 12.5 + - - +
332A ILE* 3.9 28.0 - - + -
333A ILE* 2.9 26.5 + - - +
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Residues in contact with ALA 103 (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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102A PHE* 1.3 72.3 - - - +
104A TYR* 1.3 60.0 + - - +
111A LYS* 3.5 31.1 - - + +
114A THR* 5.1 4.7 - - - -
115A MET* 3.7 29.4 - - + -
264A VAL 2.8 10.1 + - - +
265A ASP* 4.4 1.8 - - - -
266A LEU* 3.2 29.1 + - - +
333A ILE* 3.4 9.0 - - + +
335A THR* 5.2 1.1 - - + -
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Residues in contact with TYR 104 (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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102A PHE* 4.1 0.8 - - + -
103A ALA* 1.3 73.1 - - - +
105A GLY* 1.3 55.6 + - - +
111A LYS* 3.9 1.5 - - - +
266A LEU* 3.7 24.9 - - + -
267A ALA 5.6 0.4 - - - -
269A SER* 3.4 33.3 + - - -
292A LEU* 3.8 20.4 - - + +
332A ILE* 4.3 19.3 - - + -
333A ILE 2.9 7.4 + - - +
334A ALA* 3.2 7.9 - - + +
335A THR* 2.7 35.6 + - - -
348A SER* 4.9 4.7 + - - -
349A THR* 4.0 19.2 - - + -
352A TYR* 3.1 69.5 - + + +
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Residues in contact with GLY 105 (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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104A TYR* 1.3 85.9 - - - +
106A GLN* 1.3 62.1 + - - -
111A LYS* 2.8 24.4 + - - +
267A ALA 5.2 1.0 + - - -
269A SER* 2.9 29.8 + - - -
335A THR* 3.5 15.5 - - - -
349A THR* 3.9 3.1 - - - -
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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