Contacts of the helix formed by residues 85 - 98 (chain A) in PDB entry 3KXK
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 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A ILE* 5.7 0.4 - - - -
62A ILE* 3.1 10.1 - - - +
64A GLU 2.9 18.2 - - - +
65A GLN* 3.9 2.6 - - - -
66A LEU* 3.4 20.2 + - + -
71A PHE* 3.3 20.8 - - + -
84A LEU* 1.3 73.6 - - - +
86A LYS* 1.3 63.5 + - - +
87A ILE* 3.8 4.5 - - - +
88A LEU* 2.9 27.4 + - - +
89A LEU* 2.9 25.2 + - - +
114A TYR* 2.6 32.0 + - - -
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Residues in contact with LYS 86 (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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12A PHE* 6.1 3.4 - - - -
62A ILE 3.3 4.5 + - - -
63A PHE* 4.1 42.6 - - + +
64A GLU* 3.2 35.3 + - - +
65A GLN* 4.6 3.7 - - + +
85A ASP* 1.3 75.0 - - - +
87A ILE* 1.3 58.5 + - + +
89A LEU* 3.5 5.5 - - - +
90A LEU* 2.9 49.0 + - + +
239A GLY 4.7 11.3 + - - +
241A PRO* 4.0 25.9 - - + +
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Residues in contact with ILE 87 (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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65A GLN* 3.9 15.3 - - + +
85A ASP* 3.2 8.1 + - - +
86A LYS* 1.3 78.4 - - + +
88A LEU* 1.3 58.9 + - - +
90A LEU* 3.8 1.2 - - - +
91A LEU* 3.0 36.2 + - + +
114A TYR* 3.3 50.5 - - + +
241A PRO* 4.0 24.2 - - + -
243A GLN* 3.3 26.7 - - + +
244A ILE* 3.8 26.6 - - + +
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Residues in contact with LEU 88 (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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71A PHE* 3.5 30.1 - - + -
75A ARG* 3.7 6.7 - - - +
83A VAL 4.0 7.4 - - - +
84A LEU* 3.9 18.5 - - + +
85A ASP* 2.9 17.0 + - - +
87A ILE* 1.3 76.9 - - - +
89A LEU* 1.3 58.7 + - - +
91A LEU* 3.8 10.1 - - + +
92A GLU* 2.9 31.4 + - - +
111A ARG* 4.4 22.2 - - + -
114A TYR* 3.8 20.6 - - + -
115A GLU* 3.3 28.9 - - + +
118A ILE* 5.0 0.2 - - + -
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Residues in contact with LEU 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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19A LEU* 4.8 4.7 - - + -
20A VAL* 3.8 29.2 - - + +
23A ALA* 4.3 22.2 - - + -
25A TYR* 5.1 0.9 - - + -
61A ILE* 3.9 29.2 - - + -
63A PHE* 4.3 24.7 - - + -
84A LEU* 4.5 17.4 - - + +
85A ASP 2.9 18.6 + - - +
86A LYS* 3.5 4.7 - - - +
88A LEU* 1.3 77.1 - - - +
90A LEU* 1.3 60.1 + - + +
92A GLU* 3.1 7.5 + - + +
93A ILE* 2.9 41.1 + - + +
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Residues in contact with LEU 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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19A LEU* 4.1 22.0 - - + -
63A PHE* 5.5 0.9 - - + -
86A LYS* 2.9 35.8 + - + +
87A ILE 3.8 0.2 - - - +
89A LEU* 1.3 78.2 - - + +
91A LEU* 1.3 57.9 + - - +
93A ILE* 3.1 14.3 + - + +
94A PHE* 2.9 44.1 + - + -
237A ILE* 4.1 27.1 - - + -
240A ILE* 4.9 7.6 - - + -
241A PRO* 3.9 20.2 - - + -
244A ILE* 3.6 28.7 - - + -
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Residues in contact with LEU 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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87A ILE* 3.0 36.1 + - + +
88A LEU* 3.8 10.3 - - + +
90A LEU* 1.3 75.7 - - - +
92A GLU* 1.3 62.4 + - - +
94A PHE* 3.3 13.3 + - + +
95A ALA* 3.1 20.3 + - - +
107A ILE* 3.3 26.1 - - + +
110A ALA* 3.9 16.4 - - + +
111A ARG* 3.6 41.3 - - + +
114A TYR* 5.1 0.4 - - + -
244A ILE* 3.5 29.2 - - + -
247A ALA* 4.2 4.7 - - + -
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Residues in contact with GLU 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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2A LYS* 3.8 7.6 + - - -
23A ALA* 4.4 7.8 - - + +
25A TYR* 2.8 37.3 + - - -
84A LEU* 3.3 28.7 - - - +
88A LEU 2.9 17.1 + - - +
89A LEU* 3.1 6.7 + - + +
91A LEU* 1.3 77.1 - - - +
93A ILE* 1.3 60.6 + - - +
95A ALA* 3.6 7.3 + - - +
96A LEU* 3.4 28.1 + - + +
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Residues in contact with ILE 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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19A LEU* 3.2 52.5 - - + +
22A GLY* 5.3 5.2 - - - +
23A ALA* 3.8 18.6 - - + -
89A LEU* 2.9 27.5 + - + +
90A LEU* 3.1 16.1 + - + +
92A GLU* 1.3 75.0 - - - +
94A PHE* 1.3 72.7 + - + +
96A LEU* 3.2 16.9 + - - +
97A HIS* 3.0 41.8 + - + +
234A VAL* 4.9 5.2 - - + -
235A PRO* 5.3 3.8 - - + -
237A ILE* 5.9 1.6 - - + -
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Residues in contact with PHE 94 (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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90A LEU* 2.9 35.1 + - + -
91A LEU* 3.3 17.9 + - + +
93A ILE* 1.3 78.1 - - + +
95A ALA* 1.3 54.2 + - - +
97A HIS* 3.1 3.6 + - - -
98A ALA* 2.7 36.6 + - - +
107A ILE* 3.4 17.9 - - + -
234A VAL* 3.9 16.2 - - + -
237A ILE* 4.0 15.3 - - + -
240A ILE* 4.4 6.3 - - + -
244A ILE* 3.9 26.7 - - + -
247A ALA* 4.4 2.9 - - + -
248A PHE* 3.4 53.2 - + + -
251A THR* 3.8 15.4 - - + +
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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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91A LEU 3.1 16.2 + - - +
92A GLU* 3.8 9.4 - - - +
93A ILE 3.2 0.2 - - - -
94A PHE* 1.3 77.0 - - - +
96A LEU* 1.3 62.6 + - + +
98A ALA* 3.7 15.5 + - - +
104A LYS* 5.8 3.1 - - - +
107A ILE* 3.5 19.2 - - + +
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Residues in contact with LEU 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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22A GLY 4.1 5.4 - - - +
23A ALA* 3.7 39.5 - - + +
24A ASN* 4.0 18.8 - - - +
92A GLU* 3.4 21.5 + - + +
93A ILE* 3.2 10.2 + - - +
95A ALA* 1.3 80.5 - - + +
97A HIS* 1.3 61.6 + - - +
98A ALA 4.5 1.6 - - - +
217A LYS* 4.0 28.0 - - - +
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Residues in contact with HIS 97 (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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22A GLY* 4.9 4.5 - - - -
93A ILE* 3.0 41.1 + - + +
94A PHE 3.1 5.4 + - - +
96A LEU* 1.3 80.5 - - + +
98A ALA* 1.3 65.8 + - - +
99A GLY 3.3 2.3 + - - -
217A LYS* 3.3 37.4 + - + +
218A ARG* 3.5 16.5 + - - -
232A ASP* 2.8 32.8 + - - -
233A THR* 3.6 8.4 + - - -
234A VAL* 3.3 35.8 - - + +
235A PRO* 4.2 7.9 - - + +
251A THR* 4.2 4.7 - - + -
254A GLU* 3.9 4.2 - - - +
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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 PHE 2.7 21.7 + - - +
95A ALA* 3.7 13.3 - - - +
96A LEU 3.6 2.2 - - - +
97A HIS* 1.3 73.6 - - - +
99A GLY* 1.3 59.3 + - - +
100A SER 4.9 0.2 - - - -
103A ALA* 3.6 25.4 - - + -
104A LYS* 4.3 15.8 - - + +
107A ILE* 3.6 13.7 - - + -
218A ARG* 4.7 0.5 + - - -
251A THR* 4.0 5.6 - - + +
254A GLU* 3.6 8.3 - - - -
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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