Contacts of the helix formed by residues 113 - 121 (chain A) in PDB entry 4FZY
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 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A HIS* 3.5 0.7 - - - -
111A LYS* 3.7 2.0 - - - +
112A TYR* 1.3 80.3 - - - +
114A ASN* 1.3 66.6 + - - +
115A MET* 2.9 6.8 + - - +
116A ALA* 2.9 26.6 + - - +
117A LEU* 3.0 20.8 + - - +
10C G 3.4 15.2 + - - -
11C A 3.4 25.6 - - - -
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Residues in contact with ASN 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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80A HIS* 3.0 28.0 + - + +
113A SER* 1.3 70.7 - - - +
115A MET* 1.3 57.6 + - + +
117A LEU* 3.6 4.2 + - - +
118A TYR* 3.1 24.3 + - - +
133A HIS* 4.9 8.1 - - + -
139A ASP* 3.8 26.5 + - - +
142A ILE* 3.7 22.4 - - - +
143A THR* 2.8 35.8 + - - -
146A LEU* 4.5 6.1 - - - +
11C A 3.0 15.7 + - - +
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Residues in contact with MET 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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113A SER* 2.9 5.1 + - - +
114A ASN* 1.3 76.3 - - - +
116A ALA* 1.3 67.4 + - - +
117A LEU 3.3 0.2 - - - -
118A TYR* 3.4 28.0 + - + -
119A LYS* 3.3 47.2 + - - +
133A HIS* 3.7 48.2 - - + +
138A TYR* 5.2 4.5 - - + +
142A ILE* 4.7 16.6 - - + -
11C A 4.9 0.2 + - - -
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Residues in contact with ALA 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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111A LYS* 3.5 39.3 - - + +
113A SER* 2.9 23.7 + - - +
115A MET* 1.3 76.5 - - - +
117A LEU* 1.3 62.9 + - - +
119A LYS* 3.1 12.7 + - - +
120A THR* 3.0 25.1 + - - +
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Residues in contact with LEU 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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80A HIS* 3.6 16.6 - - + -
103A ALA* 4.1 17.0 - - + -
107A TRP* 5.1 3.8 - - + -
110A ILE* 3.8 21.3 - - + -
111A LYS 2.9 23.6 - - - +
112A TYR* 3.3 40.6 - - + +
113A SER 3.0 11.4 + - - +
114A ASN 3.8 3.8 - - - +
116A ALA* 1.3 75.7 - - - +
118A TYR* 1.3 67.4 + - - +
120A THR* 4.4 3.1 - - - +
121A ARG* 2.8 32.4 + - + +
123A LEU* 4.8 1.6 - - - -
146A LEU* 4.0 26.2 - - + -
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Residues in contact with TYR 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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114A ASN 3.1 15.8 + - - +
115A MET* 3.5 32.5 - - + +
116A ALA 3.2 0.2 - - - -
117A LEU* 1.3 77.3 - - - +
119A LYS* 1.3 62.8 + - + +
122A LYS* 3.2 2.1 + - - -
123A LEU* 3.0 82.2 + - + -
124A ASN* 4.3 1.9 + - - -
125A VAL* 3.9 25.5 + - + +
142A ILE* 3.7 36.6 - - + +
145A ALA* 5.4 0.2 - - + -
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Residues in contact with LYS 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 MET* 3.3 40.4 - - - +
116A ALA* 3.1 10.0 + - - +
117A LEU 3.0 0.2 - - - -
118A TYR* 1.3 82.5 - - + +
120A THR* 1.3 65.7 + - - +
122A LYS* 3.1 21.2 + - - +
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Residues in contact with THR 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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110A ILE* 4.1 33.0 - - + +
111A LYS 5.5 1.2 + - - -
116A ALA* 3.0 16.9 + - - +
117A LEU* 4.2 6.0 - - - +
119A LYS* 1.3 77.0 - - - +
121A ARG* 1.3 73.7 + - - +
122A LYS* 3.1 15.3 + - - -
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Residues in contact with ARG 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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107A TRP* 3.2 52.0 - - + +
117A LEU* 2.8 24.0 + - + +
120A THR* 1.3 84.2 + - + +
122A LYS* 1.3 74.1 + - - +
123A LEU* 3.2 16.4 + - + +
146A LEU* 4.7 6.3 - - + -
149A ASP* 2.6 41.3 + - - +
153A THR* 3.7 16.0 + - - +
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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