Contacts of the helix formed by residues 100 - 109 (chain A) in PDB entry 3KYB
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 ASN 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A SER* 3.0 24.3 + - - -
98A PRO 2.9 23.2 + - - +
99A ILE* 1.3 73.1 - - - +
101A LEU* 1.3 61.2 + - - +
102A HIS* 3.0 33.8 + - - +
103A THR* 3.0 10.3 + - - -
104A ILE* 2.9 32.0 + - - +
178A ARG* 3.2 15.7 - - + +
180A ASN 3.4 12.6 - - - +
181A TYR* 4.4 4.9 - - - +
182A ASP 3.8 16.6 - - - +
183A ASP* 3.6 14.6 - - - +
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Residues in contact with LEU 101 (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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100A ASN* 1.3 69.3 - - - +
102A HIS* 1.3 57.2 + - - +
104A ILE* 3.5 6.0 + - + -
105A ASN* 3.0 39.1 + - - +
112A CYS 3.7 14.8 - - - +
113A SER* 4.4 0.2 - - - -
114A PRO* 3.7 32.3 - - + -
117A ALA* 3.4 32.8 - - + -
178A ARG 3.3 4.1 + - - -
179A PHE 4.2 2.9 - - - +
180A ASN* 2.8 30.2 + - - +
181A TYR* 3.4 34.3 - - + +
264B GLN 3.8 2.5 - - - +
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Residues in contact with HIS 102 (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 SER* 4.5 7.9 - - - +
100A ASN* 3.0 13.5 + - - +
101A LEU* 1.3 75.9 - - - +
103A THR* 1.3 66.2 + - - +
105A ASN* 3.9 2.9 - - + +
106A GLN* 3.0 39.5 + - + +
181A TYR* 3.3 17.3 - - + -
87B LYS* 4.1 26.9 - - + -
94B VAL* 2.9 35.8 + - + -
95B PHE* 4.0 6.1 - - - -
96B SER* 4.2 3.5 + - - -
102B HIS* 3.7 22.0 + + - -
106B GLN* 3.2 23.2 + - - -
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Residues in contact with THR 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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95A PHE* 4.1 10.3 - - + -
96A SER* 2.6 31.3 + - - +
97A LEU* 4.9 0.2 - - + -
99A ILE* 3.8 16.1 - - + -
100A ASN* 3.0 29.3 + - - -
102A HIS* 1.3 79.1 + - - +
104A ILE* 1.3 58.8 + - - +
106A GLN* 3.7 3.6 - - - +
107A PHE* 2.7 34.8 + - + +
147A LEU* 5.5 0.7 - - + -
151A PHE* 3.8 33.4 - - + -
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Residues in contact with ILE 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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99A ILE* 4.1 12.3 - - + -
100A ASN 2.9 23.3 + - - +
101A LEU* 3.7 5.6 - - - +
103A THR* 1.3 76.1 - - - +
105A ASN* 1.3 65.1 + - - +
107A PHE* 4.7 1.1 - - - -
108A PHE* 3.1 37.9 + - + +
110A LYS* 5.3 0.4 - - + +
112A CYS* 5.1 1.6 - - - -
117A ALA* 4.2 16.6 - - + -
120A LEU* 4.1 25.8 - - + -
121A ILE* 4.0 16.2 - - + -
147A LEU* 4.8 5.8 - - + -
177A VAL* 3.9 28.5 - - + -
178A ARG 4.6 0.4 - - - +
179A PHE* 4.0 20.2 - - + -
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Residues in contact with ASN 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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101A LEU* 3.0 22.0 + - - +
102A HIS* 4.1 3.8 - - + +
104A ILE* 1.3 75.0 - - - +
106A GLN* 1.3 59.7 + - - +
109A SER* 3.0 10.0 + - - -
110A LYS* 2.9 48.7 + - - +
111A THR* 3.9 4.2 - - - +
112A CYS* 2.8 48.2 + - - +
181A TYR* 3.0 26.4 + - - +
93B GLN* 6.1 0.3 - - - -
94B VAL* 4.0 12.8 - - + +
106B GLN* 5.8 0.2 - - - -
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Residues in contact with GLN 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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93A GLN* 3.0 32.6 + - - +
94A VAL 3.1 29.4 + - - +
95A PHE* 3.5 21.2 - - + -
102A HIS* 3.0 27.7 + - + +
103A THR 3.8 2.2 - - - +
105A ASN* 1.3 81.4 - - - +
107A PHE* 1.3 63.1 + - - +
109A SER* 3.6 9.4 + - - +
94B VAL 5.9 0.2 + - - -
102B HIS* 3.3 12.7 + - - -
106B GLN* 4.0 43.7 - - + +
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Residues in contact with PHE 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 ASN* 4.3 12.8 - - + -
93A GLN* 5.3 4.3 + - - +
95A PHE* 3.7 24.2 - + + -
103A THR 2.7 22.5 + - - +
104A ILE 3.9 2.7 - - - +
106A GLN* 1.3 76.6 - - - +
108A PHE* 1.3 94.9 + + + +
109A SER* 3.7 2.4 + - - -
146A GLU* 3.7 33.7 - - + -
147A LEU* 3.8 15.9 - - + -
150A ALA* 3.6 22.0 - - + -
151A PHE* 3.8 14.8 - + + -
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Residues in contact with PHE 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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104A ILE* 3.1 27.7 + - + +
107A PHE* 1.3 107.0 - + - +
109A SER* 1.3 72.6 + - - +
110A LYS* 3.4 27.5 + - + +
120A LEU* 3.8 19.3 - - + -
121A ILE* 4.0 23.1 - - + -
124A LYS* 3.8 24.9 - - + -
143A ILE 5.5 0.7 - - - -
146A GLU* 3.8 29.8 - - + -
147A LEU* 4.0 18.8 - - + -
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Residues in contact with SER 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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105A ASN 3.0 10.7 + - - -
106A GLN* 3.6 7.4 + - - +
107A PHE 3.4 4.2 + - - -
108A PHE* 1.3 81.3 - - - +
110A LYS* 1.3 64.6 + - - +
92B GLY 4.5 9.6 - - - +
93B GLN* 6.0 4.7 - - - -
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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