Contacts of the strand formed by residues 102 - 115 (chain B) 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 LYS 102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B LEU* 3.1 7.0 - - - +
99B ASN 3.0 30.1 + - - +
100B ASN* 2.9 29.3 + - - +
101B GLY* 1.3 80.1 - - - +
103B PHE* 1.3 60.8 + - - +
104B TYR* 3.6 25.8 + - + +
130B GLU 4.8 0.4 - - - +
131B GLY* 3.3 20.2 - - - +
132B LEU 3.5 4.0 - - - +
133B LYS* 5.1 7.0 - - + -
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Residues in contact with PHE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B VAL* 4.4 12.3 - - + -
97B ASP 3.4 13.5 - - - -
98B LEU* 3.7 35.7 - - + -
101B GLY 5.0 0.9 - - - -
102B LYS* 1.3 71.8 - - - +
104B TYR* 1.3 63.8 + - - +
105B VAL* 4.0 4.3 - - + -
129B SER 3.4 4.7 - - - +
130B GLU 3.3 21.7 - - - -
131B GLY 3.8 1.9 + - - +
132B LEU 2.9 8.4 + - - +
133B LYS 3.3 20.4 - - - -
134B SER 3.6 2.7 - - - -
135B LYS* 3.3 63.3 - - + -
138B SER* 3.5 23.4 + - - +
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Residues in contact with TYR 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B PHE* 3.1 18.2 - - + -
97B ASP* 2.9 39.3 + - + +
99B ASN* 3.7 36.5 + - + +
100B ASN* 5.1 1.4 + - - -
102B LYS* 3.6 41.1 + - + +
103B PHE* 1.3 75.8 - - - +
105B VAL* 1.3 61.8 + - - +
129B SER 3.4 5.6 - - - -
130B GLU* 3.5 44.4 + - + +
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Residues in contact with VAL 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ALA* 5.0 0.2 - - - -
95B PHE* 3.4 12.3 - - - +
96B VAL* 3.8 26.5 - - + -
103B PHE* 4.6 2.0 - - + -
104B TYR* 1.3 80.2 - - - +
106B GLY* 1.3 62.0 - - - +
107B VAL* 3.9 17.9 - - + -
127B GLY 3.9 0.2 - - - +
128B VAL* 3.5 10.0 - - - +
129B SER 2.8 34.3 + - - +
130B GLU* 5.5 0.2 - - - +
135B LYS* 5.4 0.4 - - + +
138B SER* 4.0 29.2 - - - +
139B LEU* 3.6 25.8 - - + -
142B ALA* 3.9 8.1 - - + -
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Residues in contact with GLY 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ALA* 4.6 1.1 - - - -
94B ASP* 2.7 32.1 + - - +
95B PHE* 3.1 26.9 + - - +
105B VAL* 1.3 75.6 - - - +
107B VAL* 1.3 59.5 + - - +
126B TYR* 3.6 21.5 - - - -
127B GLY 3.7 4.3 - - - -
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Residues in contact with VAL 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B GLN* 3.8 25.6 - - + +
92B ASN 3.6 11.2 - - - +
93B VAL* 3.8 21.5 - - + -
94B ASP 4.2 0.2 - - - +
105B VAL* 3.9 10.3 - - + -
106B GLY* 1.3 79.9 - - - +
108B CYS* 1.3 72.0 + - - +
126B TYR* 3.2 10.7 - - - -
127B GLY 2.6 37.6 + - - -
139B LEU* 5.0 0.2 - - + -
142B ALA* 3.8 27.1 - - + +
143B ARG* 4.2 10.8 - - + +
146B ALA* 3.9 6.1 - - + -
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Residues in contact with CYS 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ARG* 3.5 35.9 - - - -
91B GLN* 3.4 6.4 - - - +
92B ASN* 2.9 52.7 + - - -
107B VAL* 1.3 77.0 - - - +
109B ALA* 1.3 63.8 + - - +
110B PHE* 3.9 15.0 - - - -
124B VAL* 4.4 4.7 - - + -
125B GLY 3.2 7.4 - - - +
126B TYR* 3.5 22.2 - - + -
146B ALA* 4.0 2.0 - - - -
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Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B ILE* 4.9 2.2 - - + -
90B GLN 3.4 8.5 - - - +
91B GLN* 4.1 6.7 - - + +
108B CYS* 1.3 76.9 - - - +
110B PHE* 1.3 64.1 + - - +
111B VAL* 4.0 5.1 + - + -
123B ASP 3.8 0.3 - - - +
124B VAL* 3.2 3.1 - - - -
125B GLY 2.6 36.8 + - - -
146B ALA* 3.6 29.8 - - + +
147B VAL* 3.8 18.2 - - + +
150B GLY* 4.6 0.7 - - - -
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Residues in contact with PHE 110 (chain B).
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* 3.8 30.5 - - + -
91A GLN* 3.3 47.3 - - + -
143A ARG* 4.4 4.5 - - - -
88B ILE* 3.5 4.5 - - - +
89B THR* 2.7 40.5 + - + -
90B GLN* 2.8 42.5 + - + +
92B ASN* 5.6 1.6 - - + -
108B CYS* 3.9 21.1 - - - -
109B ALA* 1.3 74.3 - - - +
111B VAL* 1.3 56.4 + - - +
122B GLU* 3.9 13.9 - - - +
123B ASP 3.3 5.2 - - - +
124B VAL* 3.5 22.2 - - + -
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Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B HIS* 3.9 21.8 - - + +
87B SER 3.4 12.3 - - - +
88B ILE* 4.8 4.7 - - + -
109B ALA* 4.6 2.7 - - + -
110B PHE* 1.3 79.8 - - - +
112B ARG* 1.3 67.6 + - - +
113B VAL* 4.6 1.3 - - + -
122B GLU* 3.2 4.9 - - - +
123B ASP 2.9 30.9 + - - -
147B VAL* 3.6 36.1 - - + +
150B GLY* 3.8 10.3 - - - -
151B LEU* 3.7 28.0 - - + +
154B ALA* 4.0 3.8 - - - +
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Residues in contact with ARG 112 (chain B).
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* 4.9 5.2 - - - -
86B HIS* 3.1 4.7 - - - +
87B SER* 2.9 41.8 + - - +
89B THR* 3.9 16.8 + - - +
110B PHE 4.3 0.4 + - - -
111B VAL* 1.3 74.8 - - - +
113B VAL* 1.3 65.6 + - - +
114B GLN* 2.9 36.8 - - - +
120B TYR* 3.5 45.3 - - + +
121B HIS 3.6 6.1 - - - +
122B GLU* 3.8 24.7 - - + -
120C TYR* 5.0 7.0 + - - +
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Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B TRP* 3.9 12.3 - - + -
85B ALA 3.1 11.0 - - - +
86B HIS* 4.0 2.2 - - + -
111B VAL* 4.6 0.9 - - + -
112B ARG* 1.3 77.0 - - - +
114B GLN* 1.3 68.2 + - - +
115B LEU* 5.3 0.2 - - + -
120B TYR* 3.2 6.0 - - - +
121B HIS 2.9 34.6 + - - +
151B LEU* 3.6 25.1 - - + -
154B ALA* 3.5 26.9 - - + -
155B LEU* 3.6 25.8 - - + -
158B PHE* 3.9 17.9 - - + -
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Residues in contact with GLN 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B PHE* 3.2 30.4 - - + -
27B GLY* 4.4 7.1 - - - -
84B TRP* 3.3 2.1 - - - -
85B ALA 2.7 39.5 + - - +
86B HIS* 4.8 0.2 - - - +
112B ARG* 2.9 29.1 - - - +
113B VAL* 1.3 77.8 - - - +
115B LEU* 1.3 70.8 + - - +
118B GLY* 3.7 17.2 + - - +
119B SER 3.1 16.2 - - - +
120B TYR* 4.2 5.1 - - + -
120C TYR* 3.7 22.5 + - - +
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A TYR* 3.8 31.4 - - + -
26B PHE* 3.8 4.3 - - - -
27B GLY 4.6 0.2 + - - -
31B TYR* 3.7 11.4 - - + +
79B PHE* 3.6 38.4 - - + -
83B GLY 3.3 7.2 - - - +
84B TRP* 3.9 9.0 - - + -
113B VAL* 5.3 0.2 - - + -
114B GLN* 1.3 83.7 - - - +
116B LYS* 1.3 67.2 + - - +
117B ASP* 2.9 14.1 + - - +
118B GLY 2.9 12.1 + - - -
119B SER* 2.9 19.2 + - - +
158B PHE* 3.4 37.7 - - + -
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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