Contacts of the strand formed by residues 84 - 99 (chain A) in PDB entry 1KN0
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 TRP 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A PHE* 3.8 2.9 - - - -
72A ILE* 4.3 14.4 - - + -
75A ALA* 3.6 29.2 - - + -
76A ASN* 2.9 26.5 + - - +
79A PHE* 3.7 20.0 - + + -
80A GLY 3.5 15.9 - - - -
81A TYR 4.2 2.7 + - - +
82A ASN 3.5 0.4 - - - -
83A GLY* 1.3 79.8 - - - +
85A ALA* 1.3 75.3 + - - +
86A HIS* 4.2 5.6 - + + -
113A VAL* 4.0 16.2 - - + -
114A GLN 3.2 10.1 - - - +
115A LEU* 3.9 5.8 - - + -
151A LEU* 3.9 34.8 - - + -
155A LEU* 4.2 11.2 - - + -
119B SER* 4.0 8.7 + - - -
121B HIS* 3.2 42.2 + + - -
157B SER* 3.8 16.4 - - - -
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Residues in contact with ALA 85 (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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26A PHE* 3.5 19.3 - - + -
84A TRP* 1.3 80.6 - - - +
86A HIS* 1.3 57.9 - - - +
113A VAL* 3.1 5.7 - - - +
114A GLN 2.6 36.3 + - - +
120B TYR* 2.7 50.5 - - + +
121B HIS* 4.0 4.0 - - - -
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Residues in contact with HIS 86 (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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84A TRP* 4.2 5.4 - + + -
85A ALA* 1.3 77.2 - - - +
87A SER* 1.3 61.0 + - - +
88A ILE* 5.5 0.6 - - - +
111A VAL* 3.9 13.3 - - + +
112A ARG 3.1 11.4 - - - +
113A VAL* 3.9 4.5 - - + -
147A VAL* 5.1 6.5 - - + -
151A LEU* 3.6 44.7 - - + +
120B TYR* 3.2 12.6 + - - -
121B HIS* 2.8 44.7 - + - +
122B GLU 3.0 49.5 + - - -
123B ASP* 4.7 7.2 - - - -
157B SER* 3.5 15.5 + - - -
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Residues in contact with SER 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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86A HIS* 1.3 76.9 - - - +
88A ILE* 1.3 67.3 + - - +
89A THR* 3.6 2.6 + - - -
111A VAL* 3.4 6.6 - - - +
112A ARG* 2.9 45.7 + - - +
112B ARG* 4.9 7.2 - - - -
120B TYR* 3.9 18.9 + - - -
122B GLU* 3.4 17.0 - - - -
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Residues in contact with ILE 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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87A SER* 1.3 75.3 - - - +
89A THR* 1.3 64.5 + - - +
90A GLN* 3.9 21.8 - - - +
91A GLN* 4.4 4.0 - - + +
109A ALA* 5.0 1.8 - - + -
110A PHE 3.5 9.0 - - - +
111A VAL* 4.7 5.6 - - + +
147A VAL* 3.5 35.7 - - + -
89B THR* 5.8 1.9 - - - +
110B PHE* 3.8 32.1 - - + -
122B GLU* 2.8 35.0 + - + +
123B ASP* 3.7 26.9 - - - -
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Residues in contact with THR 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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87A SER* 3.6 4.0 + - - -
88A ILE* 1.3 74.1 - - - +
90A GLN* 1.3 68.6 + - + +
110A PHE* 2.8 15.1 + - + -
112A ARG* 4.0 15.9 - - - +
122A GLU* 2.9 29.4 + - - +
88K ILE 5.9 1.8 - - - +
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Residues in contact with GLN 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 ILE* 3.2 7.7 - - - +
89A THR* 1.3 91.4 - - + +
91A GLN* 1.3 70.9 + - - +
92A ASN* 4.7 8.5 - - + +
109A ALA* 3.3 1.4 - - - -
110A PHE* 2.6 56.9 + - + +
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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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88A ILE* 4.4 2.8 - - + +
90A GLN* 1.3 80.7 - - - +
92A ASN* 1.3 60.4 - - - +
93A VAL 4.3 0.5 + - - -
107A VAL* 3.7 15.3 - - + +
108A CYS 3.3 15.7 - - - +
109A ALA* 3.9 8.9 - - + +
143A ARG* 2.8 72.1 + - - +
147A VAL* 3.5 13.2 - - - +
110B PHE* 3.3 39.6 - - + -
124B VAL* 3.9 1.4 - - - +
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Residues in contact with ASN 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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90A GLN* 4.2 12.3 - - + +
91A GLN* 1.3 74.8 - - - +
93A VAL* 1.3 72.4 + - - +
94A ASP* 3.3 26.5 + - - +
107A VAL* 3.6 2.2 - - - +
108A CYS* 3.0 44.6 + - - -
110A PHE* 5.6 1.8 - - + -
143K ARG* 4.4 6.6 - - - +
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Residues in contact with VAL 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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92A ASN* 1.3 80.2 + - - +
94A ASP* 1.3 64.3 + - - +
95A PHE* 4.0 6.9 - - - +
96A VAL* 3.7 29.6 - - + -
107A VAL* 3.6 24.9 - - + -
139A LEU* 4.4 7.6 - - + -
143A ARG* 3.4 41.0 - - - +
94B ASP* 5.0 0.9 - - - +
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Residues in contact with ASP 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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92A ASN* 3.3 18.8 + - - +
93A VAL* 1.3 73.5 - - - +
95A PHE* 1.3 64.1 + - + +
106A GLY 2.7 16.8 + - - +
108A CYS* 4.7 0.2 - - - -
126A TYR* 2.6 36.5 + - - +
93K VAL* 5.0 1.1 - - - +
139K LEU* 3.4 22.6 - - + +
143K ARG* 2.4 35.6 + - - -
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Residues in contact with PHE 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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93A VAL* 3.4 3.1 - - - +
94A ASP* 1.3 89.7 - - + +
96A VAL* 1.3 70.3 + - - +
97A ASP* 3.5 20.2 - - - +
104A TYR* 3.1 32.1 - - + -
105A VAL* 3.5 4.0 - - - +
106A GLY* 3.1 41.2 + - - +
130A GLU* 5.8 0.9 - - - -
135K LYS* 3.5 40.2 - - + +
136K ALA* 3.3 36.8 - - + -
139K LEU* 3.7 15.9 - - + -
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Residues in contact with VAL 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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93A VAL* 3.7 20.0 - - + -
95A PHE* 1.3 80.8 - - - +
97A ASP* 1.3 62.8 + - - +
98A LEU* 4.2 0.9 + - - +
103A PHE* 4.3 11.3 - - + -
104A TYR 3.7 4.0 - - - -
105A VAL* 3.8 15.9 - - + -
135A LYS* 4.1 28.5 - - + -
139A LEU* 3.9 19.3 - - + -
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Residues in contact with ASP 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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95A PHE* 3.5 10.1 - - - +
96A VAL* 1.3 79.4 + - - +
98A LEU* 1.3 59.9 + - - +
99A ASN* 4.1 9.9 - - - +
102A LYS 3.7 0.5 - - - +
103A PHE* 3.4 7.6 - - - -
104A TYR* 2.8 49.2 + - + +
135K LYS* 2.9 39.4 + - - -
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Residues in contact with LEU 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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96A VAL 4.2 1.2 + - - +
97A ASP* 1.3 74.8 - - - +
99A ASN* 1.3 66.4 + - - +
100A ASN 4.0 2.0 + - - +
101A GLY* 3.6 16.8 - - - +
102A LYS 3.0 36.1 - - - +
103A PHE* 3.7 32.3 - - + -
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Residues in contact with ASN 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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97A ASP* 4.7 9.8 - - - +
98A LEU* 1.3 75.2 - - - +
100A ASN* 1.3 88.0 + - - +
101A GLY 3.6 0.2 - - - -
102A LYS* 2.9 22.9 + - - +
104A TYR* 3.7 38.9 - - + +
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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