Contacts of the helix formed by residues 110 - 122 (chain A) in PDB entry 5KYT
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 ASN 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A ILE 3.4 2.8 + - - -
109A TYR* 1.3 75.6 - - - +
111A GLU* 1.3 59.3 + - - +
112A ARG* 3.2 11.3 + - - +
113A GLU* 2.8 51.3 + - - +
114A LEU* 2.8 27.0 + - - +
135A LYS* 6.1 0.7 - - - -
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Residues in contact with GLU 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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110A ASN* 1.3 74.6 - - - +
112A ARG* 1.3 54.1 + - - +
114A LEU* 4.3 4.7 - - - -
115A LEU* 2.8 37.5 + - - +
135A LYS* 4.8 15.0 - - + +
138A ASN* 2.5 50.0 + - + +
139A VAL* 3.7 17.7 - - + +
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Residues in contact with ARG 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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110A ASN* 3.2 10.4 + - - +
111A GLU* 1.3 79.4 - - - +
113A GLU* 1.3 58.6 + - + +
115A LEU* 3.9 7.7 - - - +
116A ASN* 3.0 28.6 + - - +
204A LEU* 5.4 1.9 - - - +
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Residues in contact with GLU 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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108A ILE 4.6 0.9 - - - +
109A TYR* 3.5 34.8 - - + -
110A ASN* 2.8 50.2 + - - +
112A ARG* 1.3 72.0 - - + +
114A LEU* 1.3 66.0 + - - +
116A ASN* 3.3 8.9 + - - +
117A SER* 3.0 24.1 + - - -
205A PRO* 5.6 10.5 - - + +
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Residues in contact with LEU 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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81A CYS* 4.5 9.0 - - - -
105A ALA* 3.9 27.1 - - + -
106A ASN 4.7 2.5 - - - +
109A TYR* 3.8 16.4 - - + +
110A ASN 2.8 17.3 + - - +
111A GLU* 3.7 5.2 - - - +
113A GLU* 1.3 77.1 - - - +
115A LEU* 1.3 63.9 + - - +
117A SER* 3.2 2.9 + - - -
118A MET* 3.0 36.6 + - + +
135A LYS* 3.5 50.3 - - + +
136A ILE* 3.8 22.0 - - + -
139A VAL* 4.5 3.8 - - + -
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Residues in contact with LEU 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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111A GLU 2.8 21.1 + - - +
112A ARG* 3.9 6.7 - - - +
114A LEU* 1.3 74.0 - - - +
116A ASN* 1.3 57.4 + - - +
118A MET 3.3 0.2 + - - -
119A ASN* 2.8 39.4 + - + +
139A VAL* 4.1 19.2 - - + +
142A LYS* 3.8 41.7 - - + +
143A LEU* 3.7 35.0 - - + -
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Residues in contact with ASN 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 ARG 3.0 18.4 + - - +
113A GLU* 3.5 7.6 + - - +
115A LEU* 1.3 78.8 - - - +
117A SER* 1.3 65.8 + - - +
119A ASN* 3.4 9.1 + - - +
120A ILE* 3.1 36.0 + - - +
204A LEU* 3.5 30.2 - - + +
205A PRO* 3.3 43.9 + - - +
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Residues in contact with SER 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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79A VAL* 5.8 0.5 - - - +
103A ALA* 5.9 2.1 - - - +
104A PRO 4.7 0.9 + - - -
105A ALA* 4.1 12.7 - - - +
109A TYR* 3.7 12.1 - - - -
113A GLU 3.0 14.4 + - - -
114A LEU* 3.6 7.6 - - - -
116A ASN* 1.3 80.0 - - - +
118A MET* 1.3 62.2 + - - +
120A ILE* 3.2 7.6 + - - +
121A SER* 3.0 27.9 + - - -
197A ASN* 2.9 38.9 + - - +
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Residues in contact with MET 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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79A VAL* 4.1 28.5 - - + -
105A ALA* 5.0 0.7 - - + -
114A LEU* 3.0 23.6 + - + +
117A SER* 1.3 75.4 - - - +
119A ASN* 1.3 60.5 + - - +
120A ILE 3.1 1.8 - - - -
121A SER* 3.5 6.3 - - - -
122A GLN* 2.7 34.1 + - - -
123A PRO* 3.4 15.2 - - + +
126A VAL* 4.2 9.2 - - - -
136A ILE* 3.7 30.3 - - + -
139A VAL* 3.6 32.1 - - + -
143A LEU* 3.7 22.1 - - + +
146A ILE* 4.2 7.9 - - + -
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Residues in contact with ASN 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 LEU* 2.8 29.2 + - + +
116A ASN* 3.5 10.8 + - - +
118A MET* 1.3 71.8 - - - +
120A ILE* 1.3 62.7 + - - +
122A GLN* 2.9 31.6 + - - +
142A LYS 5.4 1.0 - - - +
143A LEU* 3.7 17.9 - - + +
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Residues in contact with ILE 120 (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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116A ASN* 3.1 27.0 + - - +
117A SER* 3.5 8.7 - - - +
118A MET 3.1 0.4 - - - -
119A ASN* 1.3 83.2 - - + +
121A SER* 1.3 63.5 + - - +
122A GLN* 3.4 5.2 + - - +
195A ILE* 5.3 0.7 - - + -
197A ASN* 5.1 1.6 - - - +
205A PRO 3.5 24.7 - - - +
206A LYS* 3.9 2.2 - - - -
207A GLY* 3.7 35.9 - - - +
402A VAL* 3.8 35.9 - - + +
403A ASN* 4.6 5.6 + - + +
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Residues in contact with SER 121 (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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77A ARG* 2.6 41.8 + - - +
79A VAL* 3.9 4.6 - - - +
103A ALA* 3.6 30.9 - - - +
117A SER* 3.0 18.6 + - - -
118A MET* 3.5 8.8 - - - -
120A ILE* 1.3 76.7 - - - +
122A GLN* 1.3 61.2 + - - +
123A PRO* 3.4 7.9 - - - +
195A ILE* 4.4 18.2 - - - -
402A VAL* 5.5 0.4 - - - -
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Residues in contact with GLN 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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77A ARG* 3.1 28.9 + - - +
118A MET 2.7 16.6 + - - -
119A ASN* 2.9 44.7 + - - +
120A ILE 4.0 4.5 - - - +
121A SER* 1.3 76.1 - - - +
123A PRO* 1.3 67.9 - - - +
124A THR 3.7 1.4 + - - -
143A LEU* 4.4 8.3 - - - +
145A ILE* 3.4 32.3 - - + +
403A ASN* 5.9 3.6 - - - +
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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