Contacts of the helix formed by residues 139 - 150 (chain A) in PDB entry 1KAS
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 VAL 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A PHE* 4.1 15.0 - - - -
104A ILE 4.3 5.2 - - - +
105A GLY* 4.4 2.5 - - - -
106A SER* 3.8 36.6 - - - +
107A GLY 5.3 1.1 - - - -
108A ILE 4.6 3.6 - - - +
109A GLY* 4.1 22.0 - - - +
137A THR 3.6 1.2 + - - +
138A ILE* 1.3 72.8 - - - +
140A ASN* 1.3 59.3 + - - +
141A MET 3.2 1.7 + - - -
142A VAL* 4.0 8.1 + - - +
158A SER* 4.1 20.3 + - - +
160A ALA* 4.2 17.3 - - + -
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Residues in contact with ASN 140 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A ILE* 3.5 26.8 - - - +
139A VAL* 1.3 73.1 - - + +
141A MET* 1.3 67.9 + - - +
142A VAL 3.3 1.8 - - - -
143A ALA* 3.3 8.2 + - + +
144A GLY* 3.0 22.2 + - - -
158A SER* 3.1 26.0 - - - +
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Residues in contact with MET 141 (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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74A ILE* 3.8 11.4 - - + -
135A PRO* 3.1 37.9 - - + +
138A ILE* 3.2 38.0 + - + +
139A VAL 3.2 0.2 - - - -
140A ASN* 1.3 87.3 - - - +
142A VAL* 1.3 59.5 + - - +
144A GLY* 3.6 14.1 - - - +
145A HIS* 2.9 55.8 + - + +
148A ILE* 5.7 4.7 - - + -
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Residues in contact with VAL 142 (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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73A PHE* 3.6 35.0 - - + +
74A ILE* 3.8 24.0 - - + +
77A GLY* 3.7 32.1 - - - +
78A ILE* 4.2 2.9 - - + +
104A ILE* 3.8 31.2 - - + +
105A GLY 5.5 1.6 - - - +
139A VAL 4.0 4.4 + - - +
140A ASN 3.3 1.0 - - - -
141A MET* 1.3 76.9 - - - +
143A ALA* 1.3 58.0 + - - +
145A HIS* 3.4 2.5 + - - +
146A LEU* 3.1 29.8 + - + +
190A ALA* 4.7 3.6 - - + -
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Residues in contact with ALA 143 (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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102A ALA* 4.2 16.4 - - + -
104A ILE* 4.2 17.9 + - + +
139A VAL 5.2 0.2 + - - -
140A ASN* 3.3 9.0 + - + +
142A VAL* 1.3 77.1 - - - +
144A GLY* 1.3 64.7 + - - +
146A LEU* 4.2 1.1 - - - +
147A THR* 2.9 32.2 + - - +
156A SER* 3.8 17.9 - - - +
157A ILE 4.4 7.0 - - - +
158A SER* 4.1 14.1 - - - +
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Residues in contact with GLY 144 (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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140A ASN* 3.0 16.3 + - - -
141A MET* 3.5 15.9 + - - -
142A VAL 3.3 0.2 - - - -
143A ALA* 1.3 76.3 - - - +
145A HIS* 1.3 58.7 + - - +
147A THR* 2.6 21.5 + - - -
148A ILE* 3.2 20.8 - - - +
156A SER* 5.0 1.1 + - - -
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Residues in contact with HIS 145 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A GLU* 4.8 8.0 + - - -
69A LYS* 4.8 9.5 - - + +
70A MET* 3.7 30.3 - - + +
74A ILE* 3.7 14.0 - - + +
78A ILE* 3.7 24.0 - - + -
135A PRO* 4.5 11.2 - - + -
141A MET* 2.9 42.2 + - + +
142A VAL 3.9 2.7 - - - +
144A GLY* 1.3 77.1 - - - +
146A LEU* 1.3 61.7 + - - +
148A ILE* 3.6 13.1 + - + +
149A MET* 3.1 33.1 + - + +
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Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A GLY 4.3 7.2 - - - +
78A ILE* 4.2 33.0 - - + +
81A GLY* 4.0 24.2 - - - -
82A VAL* 4.5 0.7 - - + +
85A MET* 5.7 1.3 - - + -
102A ALA* 5.7 1.6 - - + -
104A ILE* 3.5 29.8 - - + -
142A VAL* 3.1 17.6 + - + +
143A ALA* 4.2 3.8 - - - +
144A GLY 3.4 0.2 - - - -
145A HIS* 1.3 73.0 - - - +
147A THR* 1.3 66.2 + - + +
149A MET* 3.5 5.0 - - - +
150A TYR* 3.0 52.9 + - + +
152A LEU* 4.2 10.7 - - + +
186A VAL* 4.6 10.3 - - + -
237A MET* 5.0 0.4 - - - -
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Residues in contact with THR 147 (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 GLY* 5.4 0.9 - - - -
102A ALA* 4.6 9.9 - - + +
143A ALA 2.9 21.5 + - - +
144A GLY* 2.6 26.9 + - - -
146A LEU* 1.3 74.9 - - - +
148A ILE* 1.3 55.7 + - - +
151A GLY* 2.7 32.7 + - - -
152A LEU* 2.9 43.7 + - + +
154A GLY 5.7 1.1 - - - +
156A SER* 4.0 23.1 - - - +
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Residues in contact with ILE 148 (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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141A MET* 5.7 4.9 - - + -
144A GLY* 3.2 23.1 + - - +
145A HIS* 3.9 15.0 - - + +
146A LEU 3.3 0.4 - - - -
147A THR* 1.3 84.2 + - - +
149A MET* 1.3 67.0 + - + +
151A GLY* 3.3 11.8 + - - -
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Residues in contact with MET 149 (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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61A ILE* 4.4 17.0 - - + +
62A ILE* 5.5 2.5 - - + -
78A ILE* 3.6 37.2 - - + -
82A VAL* 4.2 15.3 - - + -
145A HIS* 3.1 28.8 + - + +
146A LEU* 3.5 9.2 - - - +
148A ILE* 1.3 82.8 - - + +
150A TYR* 1.3 70.9 + - + +
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Residues in contact with TYR 150 (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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82A VAL* 3.5 37.3 + - + +
85A MET* 3.8 44.4 - - + +
86A GLN* 5.0 3.9 + - + +
92A ILE* 3.4 30.6 - - + +
146A LEU* 3.0 39.0 + - + +
149A MET* 1.3 87.9 - - + +
151A GLY* 1.3 62.8 + - - +
152A LEU* 3.6 19.9 + - + -
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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