Contacts of the helix formed by residues 98 - 107 (chain A) in PDB entry 7KAC
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 SER 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A GLY* 1.3 76.3 - - - -
99A LEU* 1.3 63.1 + - - +
100A GLN* 3.4 10.6 + - - +
101A ASP* 3.1 40.5 + - - +
102A ILE* 3.2 14.7 + - - +
140A GLY 3.5 6.3 - - - -
141A ALA* 3.3 27.3 - - - +
143A ILE 3.3 8.1 - - - -
144A LEU* 3.8 10.5 - - - +
145A ILE* 5.2 0.2 - - - -
401A W9D 3.8 5.0 - - - -
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Residues in contact with LEU 99 (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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98A SER* 1.3 71.6 - - - +
100A GLN* 1.4 56.6 + - - +
102A ILE* 3.2 11.4 + - + +
103A TYR* 2.9 34.8 + - - +
109A LEU* 4.4 15.8 - - + +
117A VAL* 3.6 41.1 - - + -
140A GLY* 3.2 8.0 + - - +
143A ILE* 3.0 37.8 + - + +
145A ILE* 3.7 26.7 - - + +
208A LEU* 3.9 23.3 - - + -
284A ILE* 5.7 0.2 - - + -
287A LEU* 4.4 8.5 - - + -
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Residues in contact with GLN 100 (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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98A SER* 3.2 9.0 + - - +
99A LEU* 1.4 77.4 - - - +
101A ASP* 1.3 69.3 + - - +
103A TYR* 3.5 32.3 + - + +
104A GLN* 3.0 54.1 + - - +
139A LYS* 5.4 4.2 - - - -
140A GLY 3.4 5.2 + - - -
141A ALA* 3.9 31.8 - - - +
207A GLU* 4.4 3.5 - - - +
178B TRP* 5.5 4.7 - - - -
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Residues in contact with ASP 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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96A ALA 4.4 8.1 - - - +
97A GLY* 3.7 4.2 - - - -
98A SER* 3.1 27.7 + - - +
100A GLN* 1.3 81.4 + - - +
102A ILE* 1.3 61.0 + - - +
104A GLN* 4.0 17.7 + - - +
105A VAL* 4.0 15.8 + - - +
291A LEU* 4.5 2.7 - - - +
401A W9D 2.6 32.9 + - + +
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Residues in contact with ILE 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 ALA* 3.6 30.1 - - + +
98A SER 3.2 16.1 + - - +
99A LEU* 3.6 11.7 - - + +
100A GLN 3.2 0.8 - - - -
101A ASP* 1.3 73.8 - - - +
103A TYR* 1.4 60.8 + - - +
104A GLN 3.2 1.8 - - - -
105A VAL* 3.0 6.8 + - - +
106A THR* 2.9 43.7 + - + +
109A LEU* 5.4 0.9 - - + -
145A ILE* 3.8 29.6 - - + -
287A LEU* 3.7 33.4 - - + +
288A LEU* 4.2 7.4 - - + -
291A LEU* 4.2 17.7 - - + -
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Residues in contact with TYR 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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99A LEU 2.9 24.4 + - - +
100A GLN* 3.5 35.0 + - + +
102A ILE* 1.4 71.6 - - - +
104A GLN* 1.3 70.7 + - + +
106A THR* 3.5 9.9 - - - -
107A GLY* 2.9 36.8 + - - +
109A LEU* 3.9 11.2 - - + -
140A GLY* 4.9 0.2 - - - -
207A GLU* 2.6 50.1 + - + +
208A LEU* 3.7 23.8 - - + +
211A LEU* 3.6 44.2 + - + +
212A GLN* 5.3 0.3 - - - -
213A PRO* 5.7 0.7 - - - +
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Residues in contact with GLN 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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100A GLN* 3.0 47.5 + - - +
101A ASP* 4.1 16.5 - - - +
102A ILE 3.2 0.4 - - - -
103A TYR* 1.3 87.9 - - + +
105A VAL* 1.3 61.2 + - + +
211A LEU* 6.2 0.4 - - - -
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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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101A ASP 4.0 11.0 - - - +
102A ILE 3.0 6.9 + - - +
104A GLN* 1.3 81.5 - - + +
106A THR* 1.3 65.2 + - - +
107A GLY 3.3 1.7 + - - -
290A LYS 5.1 0.4 - - - +
291A LEU* 3.7 26.7 - - + +
294A PRO* 4.5 24.1 - - + +
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Residues in contact with THR 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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102A ILE* 2.9 36.2 + - + +
103A TYR* 3.5 4.0 - - - +
105A VAL* 1.3 72.5 - - - +
107A GLY* 1.3 70.4 + - - +
108A SER 4.6 1.6 - - - +
109A LEU* 4.6 0.2 - - - +
287A LEU* 3.8 35.5 - - + +
290A LYS* 4.1 30.2 + - + +
291A LEU* 3.8 24.2 - - + +
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Residues in contact with GLY 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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103A TYR* 2.9 24.4 + - - +
105A VAL 3.3 2.4 + - - -
106A THR* 1.3 90.1 + - - +
108A SER* 1.3 68.3 + - - +
109A LEU* 3.4 2.8 + - - +
211A LEU* 3.6 16.8 - - - -
287A LEU* 5.5 0.2 - - - +
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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