Contacts of the helix formed by residues 83 - 92 (chain A) in PDB entry 1KIT
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 THR 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A SER* 1.3 73.6 - - - +
84A ASN* 1.3 64.3 + - - +
86A HIS* 3.1 12.0 + - + +
87A ALA* 3.0 27.1 + - + +
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Residues in contact with ASN 84 (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 SER* 3.2 10.5 + - - +
83A THR* 1.3 82.6 + - - +
85A GLN* 1.3 57.4 + - + +
87A ALA* 3.3 8.8 + - - +
88A GLN* 2.8 30.2 + - - +
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Residues in contact with GLN 85 (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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25A ALA* 5.1 2.8 - - - +
27A PHE* 3.0 36.8 - - - -
80A SER 5.0 0.3 - - - +
81A LEU* 3.8 18.9 - - + +
82A SER* 3.1 39.8 + - - +
84A ASN* 1.3 79.6 - - + +
86A HIS* 1.3 55.9 + - - +
88A GLN* 3.5 8.8 + - - +
89A ALA* 3.0 25.5 + - - +
213A ILE* 3.6 19.5 - - + +
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Residues in contact with HIS 86 (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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81A LEU* 3.7 23.3 + - + +
82A SER 3.0 27.5 + - - -
83A THR* 3.1 10.3 + - + +
85A GLN* 1.3 73.3 - - - +
87A ALA* 1.3 53.8 + - - +
89A ALA* 2.9 4.0 + - - +
90A SER* 2.7 40.5 + - - +
112A TYR* 2.8 39.6 + + - +
113A ALA 3.3 15.4 + - - -
114A ASN* 3.6 21.7 - - + +
115A GLY 5.3 1.3 + - - -
189A ASN* 3.2 30.5 + - + -
190A MET* 4.6 1.6 + - - -
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Residues in contact with ALA 87 (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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83A THR* 3.0 13.5 + - + +
84A ASN* 3.3 14.8 - - - +
86A HIS* 1.3 73.1 - - - +
88A GLN* 1.3 67.0 + - - +
90A SER* 2.9 8.6 + - - -
91A SER* 2.7 27.6 + - - +
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Residues in contact with GLN 88 (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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25A ALA* 5.3 1.0 - - - +
84A ASN 2.8 17.6 + - - +
85A GLN* 3.6 8.9 - - - +
87A ALA* 1.3 76.6 - - - +
89A ALA* 1.3 62.6 + - - +
91A SER 3.1 0.7 + - - -
92A PHE* 3.0 53.2 + - + +
93A GLY 3.8 1.4 + - - -
213A ILE* 3.4 24.9 + - + +
215A GLY 3.2 36.7 + - - +
216A ASP* 3.2 17.8 + - - +
763A ARG* 4.1 7.6 + - - +
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Residues in contact with ALA 89 (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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81A LEU* 5.9 0.2 - - + -
85A GLN 3.0 15.0 + - - +
86A HIS 2.9 12.5 + - - +
88A GLN* 1.3 78.6 - - - +
90A SER* 1.3 55.8 + - - +
93A GLY* 2.9 31.9 + - - -
94A TRP* 3.8 20.9 - - + -
112A TYR* 3.5 22.2 - - + +
160A PHE* 4.9 2.6 - - - -
162A PRO* 5.1 0.2 - - - +
213A ILE* 3.9 18.4 - - + -
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Residues in contact with SER 90 (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* 2.7 19.0 + - - +
87A ALA* 2.9 9.1 + - - -
89A ALA* 1.3 75.6 - - - +
91A SER* 1.3 58.3 + - - +
112A TYR* 5.5 0.3 + - - -
114A ASN* 5.9 2.9 - - - +
160A PHE* 5.6 7.1 - - - -
162A PRO* 3.2 23.4 - - - +
735A ASN* 4.3 6.5 + - - +
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Residues in contact with SER 91 (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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87A ALA 2.7 15.3 + - - -
88A GLN* 4.4 0.4 - - - -
90A SER* 1.3 78.5 - - - +
92A PHE* 1.3 90.8 + - - +
162A PRO* 3.5 3.2 - - - +
734A VAL* 3.5 4.5 - - - -
735A ASN* 2.8 46.0 + - - +
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Residues in contact with PHE 92 (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 GLN* 3.0 32.6 + - + +
91A SER* 1.3 98.6 - - - +
93A GLY* 1.3 60.6 + - - +
160A PHE 4.9 0.2 - - - +
162A PRO* 3.8 10.5 - - - +
214A GLN* 3.2 17.0 - - + +
215A GLY* 3.5 26.0 - - - +
733A LEU 3.6 13.8 - - - +
734A VAL* 4.1 20.6 - - + -
735A ASN 5.6 0.2 - - - -
757A THR* 4.1 18.4 - - + -
758A ASP* 5.2 1.6 - - + -
763A ARG* 3.0 54.7 - - + -
765A LEU* 4.2 10.4 - - + +
767A MET* 5.9 0.7 - - - +
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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