Contacts of the strand formed by residues 102 - 115 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98K LEU* 3.2 5.8 - - - +
99K ASN 2.9 32.0 + - - +
100K ASN* 2.8 32.7 + - - +
101K GLY* 1.3 77.0 - - - +
103K PHE* 1.3 60.9 + - - +
104K TYR* 3.4 25.5 + - + +
130K GLU 4.7 1.3 - - - +
131K GLY* 3.4 19.5 - - - +
132K LEU 3.6 4.0 - - - -
133K LYS* 5.2 6.7 - - + +
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Residues in contact with PHE 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96K VAL* 4.3 14.6 - - + -
97K ASP 3.7 11.4 - - - -
98K LEU* 3.8 36.3 - - + -
101K GLY 4.8 1.1 - - - -
102K LYS* 1.3 73.1 - - - +
104K TYR* 1.3 63.3 + - - +
105K VAL* 4.0 4.5 - - + -
129K SER 3.4 6.1 - - - +
130K GLU 3.3 22.2 - - - -
131K GLY 3.8 1.6 + - - +
132K LEU 3.0 7.7 + - - +
133K LYS 3.4 25.6 - - - -
134K SER 3.7 2.0 - - - -
135K LYS* 3.4 57.0 - - + -
138K SER* 3.6 23.5 + - - +
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Residues in contact with TYR 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95K PHE* 3.0 23.9 - - + -
97K ASP* 2.8 37.6 + - + +
99K ASN* 3.7 34.0 + - + +
100K ASN* 5.0 1.6 + - - -
102K LYS* 3.4 47.1 + - + +
103K PHE* 1.3 75.6 - - - +
105K VAL* 1.3 60.7 + - - +
129K SER 3.4 4.7 - - - -
130K GLU* 3.6 41.5 + - + +
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Residues in contact with VAL 105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95K PHE* 3.5 13.2 - - - +
96K VAL* 3.9 26.5 - - + -
103K PHE* 4.6 2.0 - - + -
104K TYR* 1.3 78.5 - - - +
106K GLY* 1.3 61.9 + - - +
107K VAL* 3.9 7.4 - - + -
128K VAL* 3.4 11.1 - - - +
129K SER* 2.8 34.6 + - - +
130K GLU* 5.4 0.6 - - - +
135K LYS* 6.1 0.2 - - + -
138K SER* 4.0 26.2 - - - +
139K LEU* 3.7 23.1 - - + -
142K ALA* 3.6 23.8 - - + -
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Residues in contact with GLY 106 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136J ALA* 4.6 1.3 - - - -
93K VAL 3.7 0.2 - - - -
94K ASP* 2.8 26.0 + - - +
95K PHE* 3.3 25.2 + - - +
105K VAL* 1.3 75.2 - - - +
107K VAL* 1.3 65.5 + - - +
126K TYR* 3.6 22.7 - - - -
127K GLY 3.6 4.5 - - - -
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Residues in contact with VAL 107 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91K GLN* 3.7 29.6 - - + +
92K ASN 3.7 11.2 - - - +
93K VAL* 3.8 21.8 - - + -
94K ASP 4.2 0.2 - - - +
105K VAL* 3.9 9.2 - - + -
106K GLY* 1.3 80.4 - - - +
108K CYS* 1.3 64.8 + - - +
126K TYR* 3.3 11.0 - - - -
127K GLY 2.8 34.8 + - - -
139K LEU* 5.0 0.4 - - + -
142K ALA* 3.7 30.5 - - + +
143K ARG* 4.2 7.0 - - + +
146K ALA* 3.5 10.9 - - + +
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Residues in contact with CYS 108 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143J ARG* 3.3 41.3 - - - -
91K GLN* 3.3 5.0 - - - +
92K ASN* 2.9 48.3 + - - -
94K ASP* 4.6 0.4 + - - -
107K VAL* 1.3 76.6 - - - +
109K ALA* 1.3 61.9 + - - +
110K PHE* 3.7 16.4 - - - -
124K VAL* 4.4 5.2 - - + -
125K GLY 3.3 7.2 - - - +
126K TYR* 3.6 21.5 - - + -
146K ALA* 4.0 1.6 - - - -
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Residues in contact with ALA 109 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88K ILE* 5.0 1.6 - - + -
90K GLN 3.3 8.3 - - - +
91K GLN* 4.0 8.3 - - + +
108K CYS* 1.3 76.2 - - - +
110K PHE* 1.3 64.8 + - - +
111K VAL* 3.8 5.5 + - + -
124K VAL* 3.4 1.8 - - - -
125K GLY* 2.7 37.1 + - - -
146K ALA* 3.7 29.7 - - + +
147K VAL* 3.9 19.5 - - + +
150K GLY* 4.4 1.4 - - - -
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Residues in contact with PHE 110 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88J ILE* 3.6 32.8 - - + -
91J GLN* 3.1 49.6 - - + -
143J ARG* 4.3 4.0 - - - -
88K ILE* 3.6 4.5 - - - +
89K THR* 2.8 42.9 + - + -
90K GLN* 2.7 42.5 + - + +
92K ASN* 5.6 1.1 - - + -
108K CYS* 3.7 22.0 - - - -
109K ALA* 1.3 74.8 - - - +
111K VAL* 1.3 60.3 + - - +
122K GLU* 4.1 5.8 - - - +
123K ASP 3.3 6.5 - - - +
124K VAL* 3.5 17.9 - - + -
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Residues in contact with VAL 111 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86K HIS* 3.9 28.9 - - + +
87K SER 3.5 11.2 - - - +
88K ILE* 4.8 6.1 - - + -
109K ALA* 3.8 4.7 + - + +
110K PHE* 1.3 79.0 - - - +
112K ARG* 1.3 64.9 + - - +
113K VAL* 4.6 1.8 - - + -
122K GLU* 3.1 5.7 - - - +
123K ASP 3.0 31.5 + - - -
147K VAL* 3.7 36.3 - - + +
150K GLY* 3.8 17.0 - - - +
151K LEU* 3.7 17.5 - - + +
154K ALA* 4.0 4.0 - - - +
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Residues in contact with ARG 112 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A TYR* 4.9 10.5 + - - -
87J SER* 4.9 5.3 - - - -
86K HIS* 3.1 2.8 - - - -
87K SER* 2.9 42.9 + - - +
89K THR* 4.0 16.8 + - - +
110K PHE 4.3 0.2 + - - -
111K VAL* 1.3 75.3 - - - +
113K VAL* 1.3 66.6 + - - +
114K GLN* 3.1 33.5 - - - +
120K TYR* 3.7 41.4 - - + +
121K HIS 3.7 5.4 - - - +
122K GLU* 3.7 25.6 - - + -
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Residues in contact with VAL 113 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84K TRP* 4.0 13.0 - - + -
85K ALA 3.2 10.8 - - - +
86K HIS* 4.1 2.9 - - + -
111K VAL* 4.6 0.9 - - + -
112K ARG* 1.3 75.7 - - - +
114K GLN* 1.3 67.6 + - - +
120K TYR* 3.2 6.1 - - - +
121K HIS 2.8 35.6 + - - +
151K LEU* 3.7 25.1 - - + -
154K ALA* 3.4 27.4 - - + -
155K LEU* 3.8 25.1 - - + +
158K PHE* 3.9 18.1 - - + -
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Residues in contact with GLN 114 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A TYR* 3.5 24.6 + - - +
26K PHE* 3.2 25.5 - - + -
27K GLY* 4.8 5.6 - - - -
84K TRP* 3.2 3.3 - - - +
85K ALA 2.6 40.5 + - - +
112K ARG* 3.1 26.5 - - - +
113K VAL* 1.3 78.0 - - - +
115K LEU* 1.3 72.8 + - - +
118K GLY* 3.8 19.3 + - - +
119K SER 3.2 17.5 - - - +
120K TYR* 4.3 4.0 - - + -
158K PHE* 5.4 0.4 - - - -
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Residues in contact with LEU 115 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81J TYR* 3.7 30.5 - - + -
26K PHE* 3.6 5.1 - - - -
31K TYR* 3.9 9.2 - - + +
79K PHE* 3.5 39.9 - - + -
83K GLY 3.2 7.4 - - - +
84K TRP* 3.8 9.9 - - + -
113K VAL* 5.4 0.2 - - + -
114K GLN* 1.3 83.5 - - - +
116K LYS* 1.3 59.2 + - - +
117K ASP* 2.9 20.8 + - - +
118K GLY 2.9 12.0 + - - -
119K SER* 2.9 18.8 + - - +
158K PHE* 3.5 37.5 - - + -
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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