Contacts of the strand formed by residues 98 - 104 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B TYR* 1.3 76.4 - - - +
99B CYS* 1.3 60.8 + - - +
258B ILE* 4.7 7.7 + - - +
260B LYS* 3.4 35.7 - - - +
322B ASP* 3.7 31.4 + - - +
323B SER* 2.7 25.7 + - - +
328B THR* 2.8 38.2 - - + +
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Residues in contact with CYS 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ILE* 3.5 19.7 - - + -
92B GLU* 3.7 28.5 - - - -
93B VAL* 3.7 16.8 - - + -
97B TYR* 4.6 4.3 - - - -
98B ASN* 1.3 76.9 - - - +
100B THR* 1.3 63.0 + - - +
260B LYS 2.9 7.5 + - - +
261B LEU* 3.3 6.6 - - - -
262B ASN* 2.9 26.0 + - - -
323B SER* 4.1 2.4 + - - -
328B THR 4.6 0.4 - - - -
329B ARG* 3.2 38.6 - - - +
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Residues in contact with THR 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ILE* 4.6 0.3 - - - +
99B CYS* 1.3 71.9 - - - +
101B ILE* 1.3 73.1 + - - +
102B PHE* 3.4 41.7 - - + -
261B LEU* 4.7 0.2 - - - -
262B ASN* 3.1 33.0 + - + +
264B VAL* 4.1 7.2 - - + -
320B LEU* 4.2 5.4 - - + +
323B SER* 3.2 18.3 + - - -
324B LEU* 4.6 3.6 - - - +
329B ARG 3.2 6.1 + - - +
330B THR* 3.4 11.1 - - - -
331B SER 3.0 23.7 + - - -
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Residues in contact with ILE 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B VAL* 4.6 2.2 - - + -
86B VAL* 4.2 28.5 - - + -
89B ILE* 3.7 38.8 - - + -
100B THR* 1.3 81.2 - - - +
102B PHE* 1.3 67.6 + - - +
115B MET* 3.0 22.8 - - + +
135B ILE* 4.4 4.3 - - + -
261B LEU* 4.3 2.7 - - + -
262B ASN 2.8 9.9 + - - +
263B LEU* 3.8 22.4 - - + -
264B VAL* 2.8 28.4 + - - +
331B SER* 3.2 13.2 - - - +
333B ILE* 4.1 16.8 - - + -
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Residues in contact with PHE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B THR* 3.4 21.5 - - + -
101B ILE* 1.3 71.4 - - - +
103B ALA* 1.3 59.3 + - - +
115B MET* 3.4 9.6 - - - +
264B VAL* 3.4 29.8 - - + -
266B LEU* 4.1 18.2 - - + -
295B LEU* 3.6 34.8 - - + -
299B ILE* 4.6 2.5 - - + -
316B LEU* 4.8 0.9 - - + -
320B LEU* 3.4 30.1 - - + -
324B LEU* 4.2 9.2 - - + -
330B THR* 4.0 15.7 - - + -
331B SER 2.7 11.7 + - - -
332B ILE* 3.9 34.3 - - + -
333B ILE* 2.9 30.2 + - - +
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Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B PHE* 1.3 74.0 - - - +
104B TYR* 1.3 59.7 + - - +
111B LYS* 3.6 32.4 - - + +
114B THR* 5.1 6.1 - - + -
115B MET* 3.5 26.7 - - + -
264B VAL 2.8 7.7 + - - +
265B ASP* 4.5 1.3 - - - +
266B LEU* 3.3 29.4 + - - +
333B ILE* 3.4 9.0 - - + +
335B THR* 5.3 1.3 - - + -
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Residues in contact with TYR 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B PHE 4.1 0.2 - - - -
103B ALA* 1.3 74.0 - - - +
105B GLY* 1.3 55.8 + - - +
111B LYS* 3.8 5.1 - - - +
266B LEU* 3.6 25.1 - - + -
267B ALA 5.4 0.7 - - - -
269B SER* 3.4 36.6 + - - -
271B ASN* 5.2 3.5 + - - -
292B LEU* 4.0 19.8 - - + +
332B ILE* 4.2 16.4 - - + -
333B ILE 2.8 12.6 + - - +
334B ALA* 3.2 9.1 - - + -
335B THR* 2.7 33.2 + - - -
348B SER* 4.9 4.0 + - - -
349B THR* 4.0 20.1 - - + +
352B TYR* 3.1 68.6 - + + +
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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