Contacts of the helix formed by residues 88 - 99 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A LEU* 4.0 9.1 - - - +
77A GLN* 5.2 8.3 - - + +
85A SER 4.7 1.7 + - - +
86A ALA 3.8 4.0 + - - -
87A ASP* 1.3 73.3 - - - +
89A PHE* 1.3 59.4 + - - +
90A PHE* 2.9 9.9 + - - +
91A GLN* 2.8 31.7 + - - +
92A GLY* 2.7 29.6 + - - -
130A LYS* 3.0 33.6 + - + +
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Residues in contact with PHE 89 (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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76A LEU* 4.0 19.6 - - + +
77A GLN* 3.0 37.6 - - + +
88A ASP* 1.3 75.5 - - - +
90A PHE* 1.3 49.8 + - - +
93A THR* 2.7 37.3 + - - +
104A ILE* 4.3 9.6 - - + -
106A ASP* 3.5 38.1 - - + -
123A TRP* 3.8 22.0 - + - -
126A ALA 4.3 1.1 - - - +
127A ALA* 3.8 38.6 - - + -
130A LYS* 3.8 20.4 - - + +
131A SER* 3.7 15.1 - - - +
135A TYR* 5.0 5.8 - + - -
137A LEU* 4.6 2.7 - - + -
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Residues in contact with PHE 90 (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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88A ASP* 2.9 13.5 + - - +
89A PHE* 1.3 77.0 - - - +
91A GLN* 1.3 80.4 + - + +
93A THR* 3.2 3.9 + - - -
94A LYS* 3.0 59.0 + - - +
130A LYS* 3.4 21.7 - - + +
132A CYS* 3.3 29.1 - - - -
461A VAL* 4.1 9.0 - - + -
462A SER* 5.3 0.2 - - - -
463A LYS* 3.5 48.2 - - + -
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Residues in contact with GLN 91 (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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86A ALA 5.6 0.7 - - - +
87A ASP* 4.3 10.8 - - + +
88A ASP* 2.8 28.8 + - - +
90A PHE* 1.3 88.3 - - + +
92A GLY* 1.3 64.2 + - - +
94A LYS* 3.1 37.0 + - - +
95A ALA* 3.0 24.5 + - - +
426A LYS* 4.0 15.0 - - - +
428A THR* 3.9 26.9 - - + +
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Residues in contact with GLY 92 (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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76A LEU* 4.0 13.7 - - - -
87A ASP* 4.0 14.1 - - - +
88A ASP 2.7 22.9 + - - -
91A GLN* 1.3 74.1 - - - +
93A THR* 1.3 55.7 + - - +
95A ALA* 3.3 8.3 + - - +
96A ALA 3.0 21.1 + - - -
358A ILE* 3.6 18.2 - - - +
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Residues in contact with THR 93 (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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76A LEU* 4.5 2.0 - - + -
89A PHE* 2.7 26.9 + - + +
90A PHE 3.2 4.4 + - - -
92A GLY* 1.3 72.2 - - - +
94A LYS* 1.3 66.6 + - - +
96A ALA* 3.5 7.6 - - - +
97A LEU* 2.9 28.7 + - - +
104A ILE* 3.8 23.3 - - + -
131A SER* 3.3 20.6 - - - +
132A CYS* 2.8 24.9 + - - +
133A CYS* 3.7 20.0 - - - -
358A ILE* 5.1 0.2 - - - -
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Residues in contact with LYS 94 (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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90A PHE* 3.0 45.5 + - - +
91A GLN* 3.1 38.8 + - - +
92A GLY 3.3 0.2 - - - -
93A THR* 1.3 77.9 + - - +
95A ALA* 1.3 63.4 + - - +
97A LEU* 3.3 2.6 + - - +
98A ALA* 3.1 22.7 + - - +
132A CYS* 4.2 9.4 - - - -
426A LYS* 4.6 16.2 - - + -
459A ILE* 3.9 31.3 - - + +
461A VAL* 4.0 15.7 - - + -
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Residues in contact with ALA 95 (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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87A ASP* 5.8 2.5 - - - +
91A GLN 3.0 13.2 + - - +
92A GLY* 3.4 10.5 - - - +
93A THR 3.2 0.2 - - - -
94A LYS* 1.3 78.0 - - - +
96A ALA* 1.3 60.1 + - - +
98A ALA* 3.4 0.9 + - - +
99A GLY 3.3 5.9 + - - -
333A HIS* 5.8 0.7 - - + -
358A ILE* 4.1 13.9 - - + -
359A GLU* 3.1 33.5 - - + +
426A LYS* 3.7 32.9 - - + +
427A SER* 4.8 3.6 - - - +
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Residues in contact with ALA 96 (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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92A GLY 3.0 6.9 + - - +
93A THR* 3.5 13.0 - - - +
94A LYS 3.2 0.2 - - - -
95A ALA* 1.3 77.0 - - - +
97A LEU* 1.3 61.1 + - - +
99A GLY* 3.0 9.2 + - - -
100A GLY 3.3 0.2 + - - -
101A THR* 2.9 43.6 + - + +
104A ILE* 4.5 5.6 - - + -
133A CYS* 5.2 1.8 - - - -
358A ILE* 3.6 39.1 - - + +
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Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A THR 2.9 15.0 + - - +
94A LYS 3.7 4.0 - - - +
96A ALA* 1.3 76.0 - - - +
98A ALA* 1.3 63.6 + - - +
100A GLY 3.1 10.0 + - - -
101A THR 3.5 16.2 - - - +
102A THR* 4.0 19.1 - - + -
132A CYS* 3.8 28.0 - - + +
133A CYS* 3.9 18.8 - - + -
446A VAL* 3.2 20.8 - - + +
448A SER* 4.1 5.2 - - - -
453A VAL* 4.0 26.0 - - + -
454A PHE* 4.4 0.2 - - - +
459A ILE* 4.1 9.4 - - + -
461A VAL* 3.6 26.9 - - + -
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Residues in contact with ALA 98 (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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94A LYS 3.1 16.1 + - - +
95A ALA 3.7 6.1 - - - +
96A ALA 3.3 0.2 - - - -
97A LEU* 1.3 77.2 - - - +
99A GLY* 1.3 58.5 + - - +
100A GLY 3.3 1.3 + - - -
359A GLU* 4.5 6.7 - - + +
426A LYS* 4.1 25.8 - - + +
443A PRO* 4.2 13.2 - - - +
454A PHE* 4.2 27.1 - - + -
459A ILE* 3.8 16.7 - - + +
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Residues in contact with GLY 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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95A ALA 3.3 5.7 + - - -
96A ALA 3.0 7.5 + - - -
98A ALA* 1.3 80.2 - - - +
100A GLY* 1.3 59.0 + - - +
101A THR* 3.4 5.0 + - - -
358A ILE 5.7 0.4 - - - -
359A GLU* 3.2 29.4 - - - +
362A MET* 3.9 18.2 + - - +
363A THR* 4.9 4.0 + - - -
412A TRP* 4.7 0.2 - - - -
443A PRO* 3.8 14.8 - - - +
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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