Contacts of the strand formed by residues 102 - 115 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A LEU* 3.0 6.3 - - - +
99A ASN 2.9 31.4 + - - +
100A ASN* 2.9 30.8 + - - +
101A GLY* 1.3 80.0 - - - +
103A PHE* 1.3 60.3 + - - +
104A TYR* 3.5 24.6 + - + +
130A GLU 5.4 0.9 - - - +
131A GLY* 3.3 19.1 - - - +
132A LEU 3.5 3.6 - - - -
133A LYS* 5.0 7.6 - - + -
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Residues in contact with PHE 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A VAL* 4.3 12.6 - - + -
97A ASP 3.4 13.7 - - - -
98A LEU* 3.7 37.9 - - + -
101A GLY 5.0 0.7 - - - -
102A LYS* 1.3 72.4 - - - +
104A TYR* 1.3 63.3 + - - +
105A VAL* 4.0 4.5 - - + -
129A SER 3.4 4.9 - - - +
130A GLU 3.2 22.5 - - - -
131A GLY 3.8 2.4 + - - +
132A LEU 2.9 8.8 + - - +
133A LYS 3.3 28.5 - - - -
134A SER 3.7 2.0 - - - -
135A LYS* 3.4 53.2 - - + -
138A SER* 3.7 21.7 + - - +
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Residues in contact with TYR 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A PHE* 3.1 16.3 - - + -
96A VAL* 3.7 0.2 - - - -
97A ASP* 2.8 43.2 + - + +
99A ASN* 3.7 36.4 + - + +
100A ASN* 5.1 1.4 + - - -
102A LYS* 3.5 43.5 + - + +
103A PHE* 1.3 75.4 - - - +
105A VAL* 1.3 59.9 + - - +
129A SER 3.4 4.5 - - - -
130A GLU* 3.6 41.3 + - + +
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Residues in contact with VAL 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A PHE* 3.5 14.4 - - - +
96A VAL* 3.8 26.2 - - + -
103A PHE* 4.6 1.6 - - + -
104A TYR* 1.3 80.2 - - - +
106A GLY* 1.3 62.2 + - - +
107A VAL* 4.0 9.0 - - + -
128A VAL* 3.5 10.2 - - - +
129A SER 2.7 33.4 + - - +
130A GLU* 5.3 0.2 - - - +
138A SER* 3.9 30.7 - - - +
139A LEU* 3.7 25.4 - - + +
142A ALA* 3.9 16.8 - - + -
136K ALA* 4.5 0.5 - - - +
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Residues in contact with GLY 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ASP* 2.7 34.5 + - - +
95A PHE* 3.1 24.9 + - - +
105A VAL* 1.3 76.7 - - - +
107A VAL* 1.3 57.3 + - - +
126A TYR* 3.6 22.2 - - - -
127A GLY 3.7 4.3 - - - -
136K ALA* 4.5 0.9 - - - -
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Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A GLN* 3.7 24.9 - - + +
92A ASN 3.6 11.0 - - - +
93A VAL* 3.6 29.6 - - + -
105A VAL* 4.0 12.8 - - + -
106A GLY* 1.3 79.5 - - - +
108A CYS* 1.3 70.2 + - - +
126A TYR* 3.3 9.4 - - - -
127A GLY 2.7 37.7 + - - +
139A LEU* 4.9 0.7 - - + -
142A ALA* 3.9 16.4 - - + +
143A ARG* 4.1 11.0 - - + +
146A ALA* 3.5 8.2 - - + +
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Residues in contact with CYS 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A GLN* 3.3 7.1 - - - +
92A ASN* 3.0 46.8 + - - -
94A ASP* 4.3 0.4 + - - -
107A VAL* 1.3 75.6 - - - +
109A ALA* 1.3 62.1 + - - +
110A PHE* 3.8 16.4 - - - -
124A VAL* 4.4 4.5 - - + -
125A GLY 3.3 7.6 - - - +
126A TYR* 3.6 21.3 - - + -
146A ALA* 4.0 2.0 - - - -
143K ARG* 3.4 42.0 - - - -
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Residues in contact with ALA 109 (chain A).
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* 5.0 2.0 - - + -
90A GLN 3.3 7.4 - - - +
91A GLN* 3.9 11.4 - - + +
108A CYS* 1.3 78.0 - - - +
110A PHE* 1.3 64.7 + - - +
111A VAL* 3.9 5.8 + - + +
123A ASP 3.7 0.2 - - - +
124A VAL* 3.2 5.0 - - - +
125A GLY 2.7 36.6 + - - -
146A ALA* 3.6 31.0 - - + +
147A VAL* 3.9 13.0 - - + +
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Residues in contact with PHE 110 (chain A).
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* 3.5 5.2 - - - +
89A THR* 2.8 41.4 + - + -
90A GLN* 2.6 49.0 + - + +
92A ASN* 5.6 1.8 - - + -
108A CYS* 3.8 21.1 - - - -
109A ALA* 1.3 73.9 - - - +
111A VAL* 1.3 58.3 + - - +
122A GLU* 4.1 6.3 - - - +
123A ASP 3.3 5.2 - - - +
124A VAL* 3.4 20.0 - - + -
88K ILE* 3.7 32.5 - - + -
91K GLN* 3.1 48.9 - - + -
143K ARG* 4.2 4.9 - - - -
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Residues in contact with VAL 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A HIS* 3.9 28.5 - - + +
87A SER 3.4 12.3 - - - +
88A ILE* 4.9 5.2 - - + -
109A ALA* 4.6 2.2 - - + +
110A PHE* 1.3 79.3 - - - +
112A ARG* 1.3 65.4 + - - +
113A VAL* 4.2 1.6 - - + -
122A GLU* 3.1 5.1 - - - +
123A ASP 2.9 31.8 + - - -
147A VAL* 3.6 24.5 - - + +
150A GLY* 3.6 17.7 - - - +
151A LEU* 3.5 29.6 - - + +
154A ALA* 4.0 3.7 - - - +
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Residues in contact with ARG 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A HIS* 3.1 3.2 - - - -
87A SER* 2.9 43.3 + - - +
89A THR* 4.0 16.4 + - - +
110A PHE 4.3 0.2 - - - -
111A VAL* 1.3 74.3 - - - +
113A VAL* 1.3 68.0 + - - +
114A GLN* 2.8 37.4 + - - +
120A TYR* 3.6 45.0 - - + +
121A HIS 3.6 5.8 - - - +
122A GLU* 3.7 24.5 - - + -
120B TYR* 5.1 7.6 + - - -
87K SER* 4.7 5.6 - - - -
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Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A TRP* 4.0 12.6 - - + -
85A ALA 3.1 10.3 - - - +
86A HIS* 3.9 2.0 - - + -
111A VAL* 4.6 1.1 - - + -
112A ARG* 1.3 78.5 - - - +
114A GLN* 1.3 67.8 + - - +
120A TYR* 3.1 7.5 - - - +
121A HIS 2.8 34.6 + - - +
151A LEU* 3.6 30.1 - - + -
154A ALA* 3.6 22.2 - - + -
155A LEU* 3.9 24.5 - - + -
158A PHE* 4.0 18.6 - - + -
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Residues in contact with GLN 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A PHE* 3.2 27.7 - - + -
27A GLY* 4.6 6.7 - - - -
84A TRP* 3.2 2.9 - - - +
85A ALA 2.6 40.6 + - - +
112A ARG* 2.8 30.3 - - - +
113A VAL* 1.3 76.8 - - - +
115A LEU* 1.3 71.0 + - - +
118A GLY* 3.9 17.8 + - - +
119A SER 3.2 16.4 - - - +
120A TYR* 4.2 3.8 - - + -
120B TYR* 3.7 23.2 + - - +
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Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A PHE* 3.6 5.4 - - - -
27A GLY 4.6 0.2 + - - -
31A TYR* 3.8 11.9 - - + +
79A PHE* 3.6 38.8 - - + -
83A GLY 3.3 8.7 - - - +
84A TRP* 3.9 8.1 - - + -
114A GLN* 1.3 83.7 - - - +
116A LYS* 1.3 64.1 + - - +
117A ASP* 2.9 16.2 + - - +
118A GLY 3.1 10.4 + - - -
119A SER* 2.8 19.0 + - - +
158A PHE* 3.5 38.1 - - + -
81K TYR* 3.8 30.5 - - + -
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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