Contacts of the helix formed by residues 111 - 123 (chain A) in PDB entry 1KYO
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 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A GLU 5.7 1.2 + - - -
90A LEU* 5.5 1.3 - - - -
107A SER* 3.9 15.5 - - - -
108A LEU* 2.9 19.1 + - - +
110A GLY* 1.3 73.8 - - - +
112A THR* 1.3 57.8 - - - +
113A ASP* 3.0 4.3 - - - +
114A LYS* 2.9 45.1 + - - +
115A SER* 3.3 9.2 + - - -
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Residues in contact with THR 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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48A ALA* 5.2 2.0 - - - -
50A VAL* 4.1 7.2 - - - +
107A SER* 4.5 2.2 - - - -
108A LEU 4.0 2.6 + - - -
109A PRO 4.1 2.9 - - - +
110A GLY* 3.0 10.7 - - - +
111A SER* 1.3 77.1 - - - +
113A ASP* 1.3 71.0 + - - +
115A SER* 3.6 11.6 - - - -
116A LEU* 3.5 23.6 + - - +
213A ILE* 3.6 45.3 - - + +
217A ASP* 4.0 20.2 - - + +
218A LEU* 4.1 13.2 - - - +
221A SER* 5.6 0.4 - - - +
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Residues in contact with ASP 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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110A GLY 5.2 3.0 - - - +
111A SER* 3.0 1.0 - - - -
112A THR* 1.3 83.5 - - - +
114A LYS* 1.3 72.7 + - - +
115A SER 3.1 1.8 - - - -
116A LEU* 3.1 19.4 + - - +
117A ASP* 3.1 20.4 + - - +
221A SER* 3.1 30.9 + - - -
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Residues in contact with LYS 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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88A GLU* 3.3 47.3 + - + +
90A LEU* 3.5 20.4 - - + +
111A SER* 2.9 34.1 + - - +
113A ASP* 1.3 85.0 - - - +
115A SER* 1.3 58.0 + - - +
117A ASP* 3.6 21.3 + - - +
118A PHE* 3.4 15.2 + - - +
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Residues in contact with SER 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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50A VAL* 4.2 22.0 - - - +
90A LEU* 3.7 11.1 - - - +
105A VAL* 4.2 20.9 + - - +
107A SER* 3.0 29.6 + - - -
111A SER 3.4 2.6 + - - -
112A THR* 3.6 10.7 + - - -
113A ASP 3.1 0.4 - - - -
114A LYS* 1.3 75.9 - - - +
116A LEU* 1.3 61.6 + - - +
118A PHE* 3.1 4.9 + - - +
119A LEU* 2.9 30.7 + - - +
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Residues in contact with LEU 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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50A VAL* 4.6 10.5 - - + -
112A THR* 3.5 17.5 - - - +
113A ASP* 3.1 14.9 + - - +
115A SER* 1.3 79.1 - - - +
117A ASP* 1.3 57.0 + - - +
119A LEU* 4.0 6.1 - - + +
120A ASN* 3.0 33.4 + - - +
207A VAL* 5.6 1.8 - - + -
218A LEU* 4.0 18.8 - - + -
221A SER* 3.5 39.0 - - - +
222A ILE* 3.9 24.5 - - + -
225A LYS* 4.3 14.1 - - + +
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Residues in contact with ASP 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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113A ASP* 3.1 18.4 + - - +
114A LYS* 3.7 28.0 + - - +
115A SER 3.2 0.2 - - - -
116A LEU* 1.3 77.1 - - - +
118A PHE* 1.3 57.3 + - - +
120A ASN* 3.7 3.6 - - - +
121A GLN* 2.8 32.7 + - - +
225A LYS* 3.9 22.5 + - - -
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Residues in contact with PHE 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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76A PHE* 4.7 3.6 - + - -
81A ASN* 3.2 41.1 - - - -
84A VAL* 3.6 18.6 - - + -
85A ALA* 3.4 38.6 - - + -
88A GLU* 6.2 1.3 - - + -
90A LEU* 3.6 22.0 - - + -
92A LEU* 3.3 30.3 - - + -
105A VAL* 4.3 9.0 - - + -
114A LYS 3.4 2.9 + - - +
115A SER 3.1 2.5 + - - +
117A ASP* 1.3 75.5 - - - +
119A LEU* 1.3 63.2 + - - +
121A GLN* 3.3 18.9 + - - +
122A SER* 3.0 45.9 + - - -
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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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50A VAL* 4.7 4.5 - - + +
51A GLY* 4.7 7.4 - - - -
52A VAL* 3.7 22.9 - - + +
76A PHE* 4.4 13.0 - - + -
103A TYR 4.1 18.6 - - - +
105A VAL* 3.8 24.9 - - + -
115A SER 2.9 17.5 + - - +
116A LEU* 4.0 8.1 - - + +
118A PHE* 1.3 78.6 - - - +
120A ASN* 1.3 59.8 + - - +
122A SER* 3.2 3.5 + - - -
123A PHE* 3.0 47.0 + - + +
207A VAL* 6.6 0.2 - - + -
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Residues in contact with ASN 120 (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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116A LEU 3.0 20.4 + - - +
117A ASP* 4.0 3.8 - - - +
119A LEU* 1.3 78.9 - - - +
121A GLN* 1.3 58.6 + - - +
122A SER 3.4 0.2 - - - -
123A PHE* 4.0 3.5 - - - +
124A ILE* 3.0 58.0 + - - +
225A LYS* 4.4 25.7 - - + +
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Residues in contact with GLN 121 (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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84A VAL* 4.0 25.4 - - - +
117A ASP* 2.8 20.8 + - - +
118A PHE* 3.5 17.5 - - - +
119A LEU 3.1 0.2 - - - -
120A ASN* 1.3 78.3 - - - +
122A SER* 1.3 62.0 + - - +
123A PHE 3.4 0.2 - - - -
125A GLN* 3.5 28.6 + - + +
126A GLN* 2.7 54.1 + - - +
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Residues in contact with SER 122 (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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76A PHE* 4.5 15.3 - - - -
81A ASN* 3.6 21.8 + - - -
118A PHE* 3.0 29.1 + - - -
119A LEU* 3.2 4.2 + - - -
121A GLN* 1.3 78.8 + - - +
123A PHE* 1.3 65.1 + - - +
124A ILE 3.6 0.4 - - - -
126A GLN* 3.9 16.5 + - - +
127A LYS* 3.1 28.1 + - - +
130A LEU* 4.7 7.5 - - - +
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Residues in contact with PHE 123 (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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52A VAL* 4.1 7.9 - - + -
54A PHE* 4.0 25.1 - + + -
72A TRP* 5.8 0.7 - + - -
76A PHE* 3.5 30.5 - + - -
103A TYR* 3.4 40.2 - + + -
119A LEU* 3.0 35.5 + - + +
120A ASN* 4.0 2.7 + - - +
122A SER* 1.3 78.5 - - - +
124A ILE* 1.3 67.9 + - + +
127A LYS* 3.6 37.0 - - - +
200A PHE* 4.3 13.0 - + + -
229A LEU* 5.3 5.0 - - - +
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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