Contacts of the strand formed by residues 120 - 129 (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 TYR 120 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26F PHE* 4.1 11.9 - + - -
85F ALA* 2.8 47.0 - - + +
86F HIS 3.1 34.4 + - - -
87F SER* 3.8 14.8 + - - -
112F ARG* 4.9 8.5 + - - -
114F GLN* 3.7 29.0 + - - +
112G ARG* 3.8 41.5 - - + +
113G VAL 3.2 12.8 - - - +
114G GLN* 4.3 2.0 - - + -
118G GLY 3.3 19.1 - - - +
119G SER* 1.3 79.8 + - - +
121G HIS* 1.3 69.1 + - - +
158G PHE* 4.7 2.0 - - - -
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Residues in contact with HIS 121 (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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81F TYR 4.1 5.4 - - - -
84F TRP* 3.2 45.0 + + - -
86F HIS* 2.8 41.1 - + + +
112G ARG* 3.5 2.1 - - - +
113G VAL* 2.7 37.1 + - + +
120G TYR* 1.3 77.3 + - - +
122G GLU* 1.3 58.2 + - - +
154G ALA* 3.9 14.1 - - - +
157G SER* 3.4 29.5 - - - -
158G PHE* 3.2 45.4 - + + -
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Residues in contact with GLU 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F HIS* 3.2 29.2 + - - -
87F SER* 3.4 20.6 - - - -
88F ILE* 2.8 54.2 + - + +
147F VAL* 5.0 0.3 - - - +
89G THR* 2.8 39.3 + - - +
110G PHE* 4.1 6.2 - - + +
111G VAL 3.2 15.7 - - - +
112G ARG* 3.7 16.4 - - + +
121G HIS* 1.3 76.4 - - - +
123G ASP* 1.3 65.9 + - - +
154G ALA* 4.5 1.8 - - - -
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Residues in contact with ASP 123 (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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86F HIS* 4.7 7.1 - - - -
88F ILE* 3.9 10.5 - - - -
147F VAL* 3.6 16.1 - - - +
148F THR* 5.4 1.4 + - - -
109G ALA 3.7 0.2 - - - +
110G PHE* 3.4 3.3 - - - +
111G VAL* 2.9 33.6 + - - +
122G GLU* 1.3 77.3 - - - +
124G VAL* 1.3 73.8 + - - +
150G GLY* 4.3 2.4 - - - +
153G ARG* 3.1 52.0 + - + +
154G ALA* 3.8 22.6 - - + +
157G SER* 4.7 2.6 + - - -
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Residues in contact with VAL 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F ILE* 4.1 2.9 - - + -
91F GLN* 3.7 9.2 - - - +
143F ARG* 3.8 20.6 - - + +
144F LYS* 4.3 7.5 - - + -
147F VAL* 3.0 36.1 - - + -
108G CYS* 4.5 7.9 - - + -
109G ALA 3.4 6.3 - - - +
110G PHE* 3.5 31.6 - - + -
123G ASP* 1.3 81.9 + - - +
125G GLY* 1.3 67.5 + - - +
126G TYR* 5.8 0.4 - - + -
149G ASP* 4.3 0.2 - - - +
150G GLY* 4.0 1.8 - - - -
153G ARG* 2.8 33.9 + - - +
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Residues in contact with GLY 125 (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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144F LYS* 4.6 0.9 - - - -
108G CYS* 3.3 7.4 - - - +
109G ALA 2.6 29.7 + - - -
124G VAL* 1.3 76.8 - - - +
126G TYR* 1.3 59.7 + - - +
146G ALA 3.1 23.8 - - - -
149G ASP* 3.4 6.1 - - - -
150G GLY* 3.3 14.5 - - - -
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Residues in contact with TYR 126 (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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136F ALA 3.7 13.9 - - - -
139F LEU* 3.2 22.0 - - + +
140F GLU* 3.6 48.4 - - + +
143F ARG* 3.6 15.0 - - + -
144F LYS* 3.9 5.4 - - + -
94G ASP* 2.4 35.2 + - - +
95G PHE* 4.2 0.9 - - - -
106G GLY* 3.6 10.1 - - - -
107G VAL 3.2 19.3 - - - -
108G CYS* 3.6 17.3 - - + -
124G VAL* 5.8 0.7 - - + -
125G GLY* 1.3 72.4 - - - -
127G GLY* 1.3 79.0 + - - +
128G VAL* 3.7 13.3 + - + +
145G GLU* 4.2 2.4 - - - +
146G ALA* 3.4 7.7 + - - -
149G ASP* 2.9 21.0 + - - +
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Residues in contact with GLY 127 (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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106G GLY* 3.7 1.0 - - - -
107G VAL 2.6 35.8 + - - -
126G TYR* 1.3 74.5 - - - +
128G VAL* 1.3 66.8 + - - +
142G ALA* 3.1 28.8 - - - +
145G GLU* 4.0 5.4 - - - -
146G ALA* 3.3 9.3 - - - +
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Residues in contact with VAL 128 (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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136F ALA* 3.5 25.4 - - + -
137F LEU* 4.5 11.0 - - + -
140F GLU* 4.8 8.5 - - - +
105G VAL 3.4 6.1 - - - +
126G TYR* 3.7 20.2 - - + +
127G GLY* 1.3 80.6 - - - +
129G SER* 1.3 66.2 + - - +
130G GLU* 3.4 28.7 - - + +
141G LYS* 2.8 38.7 + - - +
142G ALA* 3.9 4.6 - - - +
145G GLU* 3.8 6.1 + - - +
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Residues in contact with SER 129 (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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103G PHE 3.3 3.5 + - - +
104G TYR* 3.4 0.2 - - - -
105G VAL* 2.7 37.6 + - - +
128G VAL* 1.3 78.6 - - - +
130G GLU* 1.3 61.2 + - - +
131G GLY 4.6 0.3 + - - -
132G LEU* 3.8 14.2 - - - +
138G SER* 3.1 50.3 + - - -
141G LYS* 3.9 14.2 - - - +
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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