Contacts of the strand formed by residues 84 - 99 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26G PHE* 3.8 2.9 - - - -
72G ILE* 4.4 13.0 - - + -
75G ALA* 3.8 26.0 - - + -
76G ASN* 3.0 24.3 + - - +
79G PHE* 3.7 19.3 - + + -
80G GLY 3.5 16.6 - - - -
81G TYR 4.1 3.3 + - - +
82G ASN 3.5 0.6 - - - -
83G GLY* 1.3 79.9 - - - +
85G ALA* 1.3 73.7 + - - +
86G HIS* 4.3 4.0 - + + -
113G VAL* 3.8 16.4 - - + -
114G GLN 3.3 8.5 - - - +
115G LEU* 3.9 7.2 - - + -
151G LEU* 4.0 37.2 - - + -
155G LEU* 4.2 11.9 - - + -
119H SER* 3.8 13.3 + - - -
121H HIS* 3.2 41.2 + + - -
157H SER* 3.8 17.7 - - - -
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Residues in contact with ALA 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G PHE* 3.6 16.4 - - + -
84G TRP* 1.3 79.7 - - - +
86G HIS* 1.3 58.4 + - - +
113G VAL* 3.0 9.0 - - - +
114G GLN 2.7 31.9 + - - +
120H TYR* 2.7 52.5 - - + +
121H HIS* 4.1 4.5 - - - -
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Residues in contact with HIS 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G TRP* 4.3 2.9 - + + -
85G ALA* 1.3 78.0 - - - +
87G SER* 1.3 61.1 + - - +
88G ILE* 6.0 0.4 - - - +
111G VAL* 3.9 17.2 - - + +
112G ARG 2.9 12.8 - - - +
113G VAL* 4.1 2.9 - - + -
147G VAL* 5.3 4.9 - - + -
151G LEU* 3.4 42.7 - - + +
120H TYR* 3.1 17.8 + - - -
121H HIS* 2.8 48.1 - + + +
122H GLU 3.2 32.9 + - - -
123H ASP* 4.6 9.2 - - - -
157H SER* 3.5 12.2 + - - -
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Residues in contact with SER 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86G HIS* 1.3 77.1 - - - +
88G ILE* 1.3 66.7 + - - +
89G THR* 3.5 3.1 + - - -
111G VAL* 3.4 5.8 - - - +
112G ARG* 2.9 44.8 + - - +
112H ARG* 4.8 7.9 - - - -
120H TYR* 3.8 18.5 + - - -
122H GLU* 3.3 18.8 - - - -
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Residues in contact with ILE 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87G SER* 1.3 73.3 + - - +
89G THR* 1.3 68.8 + - - +
90G GLN* 3.8 24.7 - - - +
91G GLN* 4.2 3.6 - - + +
109G ALA* 4.9 2.0 - - + -
110G PHE 3.5 8.5 - - - +
111G VAL* 4.6 5.6 - - + +
147G VAL* 3.8 31.6 - - + -
89H THR* 5.7 2.3 - - - +
110H PHE* 3.5 37.0 - - + -
122H GLU* 2.6 35.5 + - + +
123H ASP* 3.8 25.4 - - - -
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Residues in contact with THR 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88F ILE 5.8 1.6 - - - +
87G SER* 3.5 4.7 + - - -
88G ILE* 1.3 76.0 - - - +
90G GLN* 1.3 68.1 + - + +
110G PHE* 2.7 17.7 + - + -
112G ARG* 4.0 15.8 - - - +
122G GLU* 2.8 28.7 + - - +
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Residues in contact with GLN 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88G ILE* 3.2 7.6 - - - +
89G THR* 1.3 90.3 - - + +
91G GLN* 1.3 71.4 + - - +
92G ASN* 4.6 9.9 - - + +
109G ALA* 3.3 1.0 - - - -
110G PHE* 2.7 54.6 + - + +
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Residues in contact with GLN 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88G ILE* 4.2 2.3 - - + +
90G GLN* 1.3 80.7 - - - +
92G ASN* 1.3 62.2 + - - +
93G VAL 4.3 0.7 + - - -
107G VAL* 3.8 15.2 - - + +
108G CYS 3.3 11.4 - - - +
109G ALA* 3.9 9.2 - - + +
143G ARG* 2.8 72.8 + - - +
147G VAL* 3.7 10.3 - - - +
110H PHE* 3.1 43.8 - - + -
124H VAL* 3.8 3.2 - - - +
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Residues in contact with ASN 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143F ARG* 4.3 7.4 - - - +
90G GLN* 4.3 13.8 - - + +
91G GLN* 1.3 75.3 - - - +
93G VAL* 1.3 69.9 + - - +
94G ASP* 3.2 30.0 + - - +
107G VAL* 4.3 2.5 - - - -
108G CYS* 2.9 41.6 + - - +
110G PHE* 5.8 0.7 - - + -
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Residues in contact with VAL 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G GLN 4.2 1.0 + - - -
92G ASN* 1.3 78.9 + - - +
94G ASP* 1.3 61.4 + - - +
95G PHE* 3.9 8.5 - - - +
96G VAL* 3.8 29.2 - - + -
107G VAL* 3.8 24.7 - - + -
139G LEU* 4.5 7.2 - - + -
143G ARG* 3.5 38.5 - - - +
94H ASP* 5.0 1.6 - - - +
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Residues in contact with ASP 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F VAL* 5.1 0.5 - - - +
139F LEU* 3.3 21.4 - - + +
143F ARG* 2.5 33.9 + - - -
92G ASN* 3.2 19.8 + - - +
93G VAL* 1.3 73.0 - - - +
95G PHE* 1.3 60.9 + - + +
106G GLY 2.7 18.2 + - - +
108G CYS* 4.8 0.4 - - - -
126G TYR* 2.4 35.6 + - - +
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Residues in contact with PHE 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F LYS* 3.3 47.1 - - + +
136F ALA* 3.2 40.2 - - + -
139F LEU* 3.6 23.3 - - + -
93G VAL* 3.4 3.3 - - - +
94G ASP* 1.3 81.7 - - + +
96G VAL* 1.3 71.5 + - - +
97G ASP* 3.5 15.5 - - - +
104G TYR* 2.9 37.9 - - + -
105G VAL* 3.5 2.8 - - - +
106G GLY* 3.2 30.1 + - - +
130G GLU* 5.9 0.2 - - - -
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Residues in contact with VAL 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93G VAL* 3.8 11.4 - - + -
95G PHE* 1.3 80.7 - - - +
97G ASP* 1.3 63.4 + - - +
98G LEU* 5.5 0.2 - - - +
103G PHE* 4.3 12.2 - - + -
104G TYR 3.9 3.6 - - - -
105G VAL* 4.0 14.8 - - + -
135G LYS* 4.2 27.1 - - + -
139G LEU* 3.8 27.8 - - + -
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Residues in contact with ASP 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F LYS* 2.7 42.7 + - - -
95G PHE* 3.5 8.2 - - - +
96G VAL* 1.3 80.0 + - - +
98G LEU* 1.3 61.2 + - - +
99G ASN* 4.1 10.8 - - - +
102G LYS 3.7 0.2 - - - +
103G PHE* 3.3 9.7 - - - -
104G TYR* 2.9 42.7 + - + +
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Residues in contact with LEU 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96G VAL 4.2 0.8 + - - +
97G ASP* 1.3 74.8 - - - +
99G ASN* 1.3 64.1 + - - +
100G ASN 4.0 2.1 + - - +
101G GLY* 3.7 15.7 - - - +
102G LYS 3.1 32.3 - - - +
103G PHE* 3.5 35.2 - - + -
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Residues in contact with ASN 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97G ASP* 4.1 10.3 - - - +
98G LEU* 1.3 76.5 - - - +
100G ASN* 1.3 89.3 + - - +
102G LYS* 2.9 21.4 + - - +
104G TYR* 3.7 40.5 - - + +
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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