Contacts of the helix formed by residues 108 - 119 (chain A) in PDB entry 1KYH
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 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A TRP* 5.4 0.3 - - - -
106A PRO* 3.0 28.7 + - + +
107A GLN* 1.3 79.0 - - - +
109A GLU* 1.3 64.1 + - - +
110A SER* 3.6 10.3 + - - -
111A VAL* 3.2 33.8 + - - +
112A GLN* 3.2 16.6 + - - +
130A GLY 4.7 0.5 + - - +
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Residues in contact with GLU 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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108A THR* 1.3 75.3 - - - +
110A SER* 1.3 57.4 + - - +
112A GLN* 3.1 11.1 + - - +
113A GLN* 2.9 33.7 + - + +
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Residues in contact with SER 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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84A TRP* 5.2 7.7 - - - +
88A ALA* 3.4 16.3 - - - +
108A THR* 3.2 10.3 + - - -
109A GLU* 1.3 79.4 - - - +
111A VAL* 1.3 61.9 + - - +
113A GLN* 3.2 12.2 + - - +
114A ALA* 3.1 17.8 + - - +
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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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84A TRP* 3.9 29.8 - - + -
101A ILE* 4.6 2.2 - - + -
105A LEU* 4.1 19.1 - - + -
106A PRO* 3.2 23.3 - - + +
108A THR* 3.2 18.0 + - - +
110A SER* 1.3 76.0 - - - +
112A GLN* 1.3 59.0 + - - +
114A ALA* 3.1 8.5 + - - +
115A VAL* 2.9 27.4 + - + +
130A GLY 3.9 19.5 - - - +
131A ALA* 3.9 20.2 - - + +
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Residues in contact with GLN 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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108A THR 3.2 11.5 + - - +
109A GLU* 3.1 13.8 + - - +
111A VAL* 1.3 79.7 - - - +
113A GLN* 1.3 56.4 + - + +
115A VAL* 3.3 6.7 + - - +
116A ASP* 3.0 36.2 + - - +
130A GLY 4.2 4.0 - - - +
131A ALA* 3.0 32.4 + - - +
133A ALA* 3.7 19.9 - - + +
135A ARG* 2.9 45.8 + - - +
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Residues in contact with GLN 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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88A ALA* 3.8 23.2 + - + +
109A GLU* 2.9 22.0 + - + +
110A SER* 3.3 11.2 - - - +
111A VAL 3.2 0.2 - - - -
112A GLN* 1.3 73.6 - - - +
114A ALA* 1.3 65.7 + - - +
116A ASP* 3.3 18.8 + - - +
117A HIS* 3.0 34.3 + - - -
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Residues in contact with ALA 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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84A TRP* 3.6 24.5 - - + +
87A ALA* 3.5 23.1 - - + +
88A ALA* 3.7 2.2 - - - +
101A ILE* 3.8 14.4 - - + -
110A SER 3.1 10.5 + - - +
111A VAL* 3.1 10.5 + - - +
113A GLN* 1.3 78.3 - - - +
115A VAL* 1.3 57.2 + - - +
117A HIS* 3.2 3.1 + - - +
118A VAL* 2.9 35.0 + - - +
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Residues in contact with VAL 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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101A ILE* 3.9 19.7 - - + -
111A VAL 2.9 21.0 + - - +
112A GLN* 3.4 16.2 - - - +
113A GLN 3.2 0.2 - - - -
114A ALA* 1.3 77.2 - - - +
116A ASP* 1.3 62.1 + - - +
118A VAL* 3.2 6.7 + - + +
119A LEU* 2.9 42.8 + - + +
127A LEU* 4.0 24.0 - - + -
131A ALA* 4.0 22.4 - - + +
135A ARG* 3.5 20.4 - - - +
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Residues in contact with ASP 116 (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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112A GLN* 3.0 21.1 + - - +
113A GLN* 3.3 25.5 + - - +
115A VAL* 1.3 77.7 - - - +
117A HIS* 1.3 63.3 + - + +
119A LEU* 3.4 15.4 + - - +
120A THR* 3.6 15.4 - - - +
135A ARG* 2.7 39.9 + - - -
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Residues in contact with HIS 117 (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* 3.0 29.6 - - + +
88A ALA 3.0 22.5 + - - -
89A ASP 3.9 6.1 + - - -
90A ALA* 3.7 23.1 - - - +
91A GLN* 3.7 25.6 + - + +
92A LEU* 4.6 4.8 + - + +
113A GLN* 3.0 28.3 + - - +
114A ALA 3.2 2.4 + - - +
116A ASP* 1.3 77.9 - - + +
118A VAL* 1.3 60.6 + - + +
120A THR* 2.7 29.4 + - - +
121A ALA* 4.3 1.0 + - - +
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Residues in contact with VAL 118 (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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33A LEU* 3.8 28.9 - - + -
87A ALA* 4.7 6.7 - - + -
92A LEU* 4.4 18.2 - - + -
99A ILE* 3.7 29.2 - - + -
101A ILE* 4.9 4.9 - - + -
114A ALA 2.9 21.4 + - - +
115A VAL* 3.6 8.1 - - - +
117A HIS* 1.3 77.2 - - + +
119A LEU* 1.3 58.5 + - - +
120A THR 3.1 0.2 - - - -
121A ALA* 3.1 25.6 + - - +
125A VAL* 3.7 25.1 - - + +
140A ARG* 4.2 3.3 + - - -
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Residues in contact with LEU 119 (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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115A VAL* 2.9 37.3 + - + +
116A ASP* 3.7 8.5 - - - +
117A HIS 3.3 0.4 - - - -
118A VAL* 1.3 76.5 - - - +
120A THR* 1.3 55.5 + - + +
121A ALA 3.2 0.7 - - - -
125A VAL* 4.1 22.7 - - + -
127A LEU* 5.4 0.4 - - + -
135A ARG* 4.0 12.6 - - - +
137A TYR* 4.2 11.2 - - + -
138A PRO* 3.9 34.7 - - + +
140A ARG* 2.6 52.6 + - - +
144A VAL* 3.9 18.6 - - + -
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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