Contacts of the helix formed by residues 88 - 99 (chain B) in PDB entry 1KCX
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 ASP 88 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B LEU* 3.9 11.7 - - - +
77B GLN* 5.1 8.3 - - + +
85B SER 4.9 1.5 + - - +
86B ALA 3.8 4.6 + - - +
87B ASP* 1.3 72.8 - - - +
89B PHE* 1.3 60.7 + - - +
90B PHE* 2.8 19.3 + - - +
91B GLN* 2.9 22.9 + - - +
92B GLY* 2.7 33.3 + - - -
130B LYS* 3.4 29.1 + - + +
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Residues in contact with PHE 89 (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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76B LEU* 3.8 19.7 - - + +
77B GLN* 2.8 41.9 - - + +
88B ASP* 1.3 75.9 - - - +
90B PHE* 1.3 50.7 + - - +
93B THR* 2.6 40.0 + - + +
104B ILE* 4.1 11.2 - - + -
106B ASP* 3.6 40.4 - - + -
123B TRP* 3.9 20.0 - + - -
126B ALA 4.1 0.4 - - - -
127B ALA* 3.6 38.4 - - + -
130B LYS* 3.8 20.4 - - + +
131B SER* 3.6 7.8 - - - +
135B TYR* 5.3 3.4 - + - -
137B LEU* 4.6 5.2 - - + -
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Residues in contact with PHE 90 (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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88B ASP* 2.8 16.2 + - - +
89B PHE* 1.3 71.3 - - - +
91B GLN* 1.3 97.6 + - + +
93B THR* 3.3 4.0 + - - -
94B LYS* 3.0 43.5 + - - +
130B LYS* 3.5 22.3 - - + +
132B CYS* 3.6 24.2 - - - -
461B VAL* 4.1 12.1 - - + -
463B LYS* 3.4 42.8 - - + -
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Residues in contact with GLN 91 (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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86B ALA 5.7 0.2 - - - +
87B ASP* 4.3 11.7 - - + +
88B ASP* 2.9 29.1 + - - +
90B PHE* 1.3 96.8 - - + +
92B GLY* 1.3 63.9 + - - +
94B LYS* 3.3 33.4 + - - +
95B ALA* 3.0 24.7 + - - +
426B LYS 3.8 19.7 - - - +
428B THR* 4.1 21.8 - - + +
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Residues in contact with GLY 92 (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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76B LEU* 4.1 14.4 - - - -
87B ASP* 4.0 13.5 - - - +
88B ASP 2.7 22.7 + - - -
91B GLN* 1.3 72.7 - - - +
93B THR* 1.3 56.5 + - - +
95B ALA* 3.4 6.5 + - - +
96B ALA 3.0 20.8 + - - -
333B HIS* 5.3 0.2 - - - -
358B ILE* 3.5 19.5 - - - +
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Residues in contact with THR 93 (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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76B LEU* 4.3 2.5 - - + -
89B PHE* 2.6 28.0 + - + +
90B PHE 3.3 6.1 + - - -
92B GLY* 1.3 73.1 - - - +
94B LYS* 1.3 65.2 + - - +
96B ALA* 3.6 7.2 - - - +
97B LEU* 3.0 29.3 + - - +
104B ILE* 3.8 28.7 - - + -
131B SER* 3.5 17.5 - - - +
132B CYS* 2.8 26.1 + - - +
133B CYS* 3.8 15.2 - - - -
358B ILE* 5.0 0.2 - - - -
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Residues in contact with LYS 94 (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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90B PHE* 3.0 44.3 + - - +
91B GLN* 3.3 31.7 + - - +
92B GLY 3.2 0.2 - - - -
93B THR* 1.3 81.2 + - - +
95B ALA* 1.3 62.2 + - - +
97B LEU* 3.3 4.9 + - - +
98B ALA* 3.1 21.8 + - - +
132B CYS* 4.2 10.1 - - - -
426B LYS* 5.0 21.8 + - + +
459B ILE* 3.1 37.3 - - + +
461B VAL* 4.0 7.4 - - + -
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Residues in contact with ALA 95 (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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87B ASP* 6.1 0.9 - - - +
91B GLN 3.0 12.8 + - - +
92B GLY* 3.7 5.6 - - - +
94B LYS* 1.3 78.5 - - - +
96B ALA* 1.3 63.3 + - - +
98B ALA* 3.4 2.4 + - - -
99B GLY 3.2 6.9 + - - -
333B HIS* 6.0 0.7 - - + -
358B ILE* 4.2 8.7 - - + -
359B GLU* 3.0 37.7 - - + +
426B LYS* 3.6 36.1 - - + -
427B SER* 4.7 3.1 - - - +
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Residues in contact with ALA 96 (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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92B GLY 3.0 6.9 + - - +
93B THR* 3.6 11.7 - - - +
94B LYS 3.2 0.2 - - - -
95B ALA* 1.3 74.9 - - - +
97B LEU* 1.3 60.5 + - + +
99B GLY* 2.9 13.2 + - - -
100B GLY 3.2 0.2 + - - -
101B THR* 2.9 43.6 + - + +
104B ILE* 4.5 4.9 - - + -
133B CYS* 5.4 1.8 - - - -
358B ILE* 3.5 41.8 - - + +
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Residues in contact with LEU 97 (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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93B THR 3.0 15.9 + - - +
94B LYS 3.6 4.3 - - - +
96B ALA* 1.3 76.5 - - - +
98B ALA* 1.3 62.4 + - - +
100B GLY 3.1 9.9 + - - -
101B THR 3.3 15.9 - - - +
102B THR* 4.0 13.2 - - + -
132B CYS* 3.6 39.7 - - + +
133B CYS* 3.9 19.1 - - + -
446B VAL* 3.4 21.0 - - + +
448B SER* 4.1 14.8 - - - -
453B VAL* 4.2 20.6 - - + +
454B PHE* 4.6 2.3 - - + +
459B ILE* 5.3 1.6 - - + -
461B VAL* 3.6 21.1 - - + -
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Residues in contact with ALA 98 (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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94B LYS 3.1 13.4 + - - +
95B ALA* 3.6 12.8 - - - +
96B ALA 3.2 0.2 - - - -
97B LEU* 1.3 77.1 - - - +
99B GLY* 1.3 59.4 + - - +
100B GLY 3.6 0.5 + - - -
359B GLU* 4.6 8.0 - - + +
426B LYS* 4.4 17.7 - - + +
443B PRO* 4.3 10.6 - - - +
454B PHE* 4.5 28.8 - - + -
459B ILE* 4.7 18.5 - - + +
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Residues in contact with GLY 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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95B ALA 3.2 6.2 + - - -
96B ALA 2.9 7.9 + - - -
98B ALA* 1.3 78.5 - - - +
100B GLY* 1.3 58.0 + - - +
101B THR* 3.4 4.9 + - - -
358B ILE 5.8 0.2 - - - -
359B GLU* 3.3 28.3 - - - +
362B MET* 3.7 20.3 + - - +
363B THR* 5.0 3.5 + - - -
412B TRP* 4.5 0.2 - - - -
443B PRO* 3.6 15.6 - - - +
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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