Contacts of the strand formed by residues 102 - 115 (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 LYS 102 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98G LEU* 3.1 6.5 - - - +
99G ASN 2.9 31.6 + - - +
100G ASN* 2.8 32.4 + - - +
101G GLY* 1.3 78.6 - - - +
103G PHE* 1.3 59.9 + - - +
104G TYR* 3.5 25.6 + - + +
130G GLU 5.4 0.9 - - - +
131G GLY* 3.4 19.5 - - - +
132G LEU 3.6 3.6 - - - -
133G LYS* 5.1 7.0 - - + +
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Residues in contact with PHE 103 (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* 4.3 12.6 - - + -
97G ASP 3.3 14.1 - - - -
98G LEU* 3.5 38.6 - - + -
101G GLY 5.3 0.4 - - - -
102G LYS* 1.3 71.4 - - - +
104G TYR* 1.3 62.8 + - - +
105G VAL* 3.9 4.9 - - + -
129G SER 3.3 5.7 - - - +
130G GLU 3.3 20.8 - - - -
131G GLY 3.8 1.9 + - - +
132G LEU 3.0 8.6 + - - +
133G LYS 3.4 24.0 - - - -
134G SER 3.6 2.0 - - - -
135G LYS* 3.4 58.3 - - + -
138G SER* 3.5 22.5 + - - +
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Residues in contact with TYR 104 (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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95G PHE* 2.9 27.9 - - + -
97G ASP* 2.9 29.6 + - + +
99G ASN* 3.7 34.9 + - + +
100G ASN* 5.0 1.4 + - - -
102G LYS* 3.5 46.1 + - + +
103G PHE* 1.3 76.1 - - - +
105G VAL* 1.3 60.5 + - - +
129G SER 3.4 4.7 - - - -
130G GLU* 3.5 40.8 + - + +
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Residues in contact with VAL 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F ALA* 4.9 0.2 - - - -
95G PHE* 3.5 12.1 - - - +
96G VAL* 4.0 26.7 - - + -
103G PHE* 4.6 2.0 - - + -
104G TYR* 1.3 78.2 - - - +
106G GLY* 1.3 61.4 + - - +
107G VAL* 3.8 8.1 - - + -
127G GLY 3.8 0.2 - - - +
128G VAL* 3.4 11.6 - - - +
129G SER* 2.7 32.9 + - - +
135G LYS* 6.2 0.4 - - + -
138G SER* 3.9 28.9 - - - +
139G LEU* 3.8 24.2 - - + -
142G ALA* 3.6 21.5 - - + -
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Residues in contact with GLY 106 (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* 4.5 1.3 - - - -
94G ASP* 2.7 34.8 + - - +
95G PHE* 3.2 26.3 + - - +
105G VAL* 1.3 75.4 - - - +
107G VAL* 1.3 57.3 + - - +
126G TYR* 3.6 21.3 - - - -
127G GLY 3.7 3.8 - - - -
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Residues in contact with VAL 107 (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* 3.8 37.0 - - + +
92G ASN 3.8 7.4 - - - +
93G VAL* 3.8 22.9 - - + -
94G ASP 4.1 0.2 - - - +
105G VAL* 3.8 10.5 - - + -
106G GLY* 1.3 79.1 - - - +
108G CYS* 1.3 63.7 + - - +
126G TYR* 3.2 10.5 - - - -
127G GLY 2.6 36.1 + - - -
139G LEU* 5.0 0.4 - - + -
142G ALA* 3.7 31.0 - - + +
143G ARG* 4.1 7.4 - - + +
146G ALA* 3.8 7.4 - - + -
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Residues in contact with CYS 108 (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* 3.3 41.7 - - - -
91G GLN* 3.3 4.0 - - - +
92G ASN* 2.9 49.1 + - - -
94G ASP* 4.3 0.6 + - - +
107G VAL* 1.3 76.6 - - - +
109G ALA* 1.3 61.4 + - - +
110G PHE* 3.8 17.0 - - - -
124G VAL* 4.5 4.5 - - + -
125G GLY 3.3 7.2 - - - +
126G TYR* 3.6 22.2 - - + -
146G ALA* 4.1 1.6 - - - -
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Residues in contact with ALA 109 (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* 4.9 2.2 - - + -
90G GLN 3.3 8.3 - - - +
91G GLN* 3.9 15.5 - - + +
108G CYS* 1.3 75.4 - - - +
110G PHE* 1.3 64.8 + - - +
111G VAL* 3.9 5.3 + - + +
123G ASP 3.7 0.3 - - - +
124G VAL* 3.4 2.0 - - - -
125G GLY* 2.6 38.5 + - - -
146G ALA* 3.8 28.0 - - + +
147G VAL* 3.9 12.6 - - + +
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Residues in contact with PHE 110 (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* 3.7 34.3 - - + -
91F GLN* 3.0 49.1 - - + -
143F ARG* 4.4 4.0 - - - -
88G ILE* 3.5 4.2 - - - +
89G THR* 2.7 48.4 + - + -
90G GLN* 2.7 42.2 + - + +
92G ASN* 5.8 1.1 - - + -
108G CYS* 3.8 22.0 - - - -
109G ALA* 1.3 73.4 - - - +
111G VAL* 1.3 58.3 + - - +
122G GLU* 4.1 6.1 - - - +
123G ASP 3.4 4.9 - - - +
124G VAL* 3.5 17.9 - - + -
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Residues in contact with VAL 111 (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* 3.9 30.7 - - + +
87G SER 3.4 13.2 - - - +
88G ILE* 4.9 5.8 - - + -
109G ALA* 4.5 4.0 - - + +
110G PHE* 1.3 79.9 - - - +
112G ARG* 1.3 65.0 + - - +
113G VAL* 4.7 1.1 - - + -
122G GLU* 3.2 5.1 - - - +
123G ASP 2.9 31.5 + - - -
147G VAL* 3.6 35.9 - - + +
150G GLY* 3.8 10.1 - - - +
151G LEU* 3.7 23.1 - - + +
154G ALA* 4.0 3.8 - - - +
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Residues in contact with ARG 112 (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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87F SER* 5.0 4.6 - - - -
86G HIS* 2.9 5.0 - - - -
87G SER* 2.9 43.0 + - - +
89G THR* 4.0 15.5 - - - +
110G PHE 4.3 0.2 + - - -
111G VAL* 1.3 73.4 - - - +
113G VAL* 1.3 66.7 + - - +
114G GLN* 2.7 38.8 + - - +
120G TYR* 3.8 41.3 - - + +
121G HIS 3.5 7.2 - - - +
122G GLU* 3.7 26.0 - - + -
120H TYR* 5.0 7.8 + - - -
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Residues in contact with VAL 113 (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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84G TRP* 3.8 14.4 - - + -
85G ALA 3.0 16.2 - - - +
86G HIS* 4.1 1.6 - - + -
111G VAL* 4.7 0.9 - - + -
112G ARG* 1.3 78.1 - - - +
114G GLN* 1.3 63.7 + - - +
120G TYR* 3.2 6.3 - - - +
121G HIS 2.7 37.6 + - - +
151G LEU* 3.7 23.3 - - + -
154G ALA* 3.3 28.7 - - + -
155G LEU* 3.7 25.8 - - + +
158G PHE* 4.1 17.5 - - + -
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Residues in contact with GLN 114 (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* 3.3 29.3 - - + -
27G GLY* 4.4 6.5 - - - -
84G TRP* 3.3 0.3 - - - -
85G ALA 2.7 39.6 + - - +
112G ARG* 2.7 33.1 + - - +
113G VAL* 1.3 75.8 - - - +
115G LEU* 1.3 70.2 + - - +
118G GLY* 4.0 18.7 + - - +
119G SER 3.2 15.3 - - - +
120G TYR* 4.3 2.9 - - + +
120H TYR* 3.7 24.5 + - - +
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Residues in contact with LEU 115 (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* 3.9 23.3 - - + -
82F ASN* 4.6 0.2 - - + -
26G PHE* 3.6 4.7 - - - -
31G TYR* 3.7 16.4 - - + +
79G PHE* 3.6 36.8 - - + -
83G GLY 3.4 12.1 - - - +
84G TRP* 3.9 6.7 - - + -
113G VAL* 5.4 0.2 - - + -
114G GLN* 1.3 83.5 - - - +
116G LYS* 1.3 64.8 + - - +
117G ASP* 3.0 16.1 + - - +
118G GLY 3.1 10.7 + - - -
119G SER* 2.9 19.7 + - - +
158G PHE* 3.4 36.8 - - + -
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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