Contacts of the helix formed by residues 110 - 118 (chain D) in PDB entry 6UZA
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105D ALA* 2.9 24.6 + - + +
108D TYR* 3.6 1.6 + - + -
109D GLY* 1.3 72.3 - - - +
111D ILE* 1.3 63.4 + - - +
112D PRO* 3.6 13.2 - - - +
113D VAL* 3.4 31.5 + - - +
114D VAL* 3.2 26.7 + - - +
148D ILE* 4.5 0.2 - - - -
896D TYR* 3.8 41.3 - - + +
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Residues in contact with ILE 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D GLY* 2.9 11.0 + - - +
110D ASN* 1.3 71.6 - - - +
112D PRO* 1.4 65.5 - - + +
114D VAL* 3.3 4.3 + - - +
115D ARG* 2.9 46.5 + - - +
147D GLU* 3.3 41.7 - - + +
148D ILE* 3.8 21.5 - - + -
151D LEU* 4.3 13.4 - - + +
893D SER* 3.6 16.4 - - - +
896D TYR* 5.0 0.2 - - - +
897D GLU* 3.6 24.7 - - + +
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Residues in contact with PRO 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D ASN* 3.6 12.3 - - - +
111D ILE* 1.4 92.3 - - + +
113D VAL* 1.3 58.0 + - + +
115D ARG* 3.3 20.9 + - + +
116D LYS* 2.9 29.5 + - - +
896D TYR 4.6 11.7 - - - +
897D GLU* 4.8 5.2 - - + -
900D GLU* 3.4 52.5 - - + +
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Residues in contact with VAL 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D ARG* 3.9 20.6 - - + +
105D ALA* 3.8 15.5 - - + -
110D ASN* 3.4 35.8 + - - +
111D ILE 3.3 0.6 - - - -
112D PRO* 1.3 77.8 - - + +
114D VAL* 1.3 58.4 + - - +
116D LYS* 3.3 10.4 + - - +
117D MET* 2.9 51.2 + - + +
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Residues in contact with VAL 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D PHE* 4.1 26.9 - - + -
105D ALA* 3.8 28.3 - - + +
106D ALA* 4.1 8.5 - - + +
110D ASN 3.2 15.9 + - - +
111D ILE* 3.3 8.7 + - - +
112D PRO 3.3 0.2 - - - -
113D VAL* 1.3 75.4 - - - +
115D ARG* 1.3 56.7 + - - +
117D MET* 4.4 0.2 - - - +
118D LEU* 2.9 45.1 + - + +
148D ILE* 4.3 18.4 - - + -
151D LEU* 3.7 18.4 - - + -
152D LEU* 5.0 3.8 - - + -
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Residues in contact with ARG 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ILE* 2.9 29.9 + - - +
112D PRO* 3.3 32.5 + - + +
114D VAL* 1.3 77.1 - - - +
116D LYS* 1.3 61.7 + - - +
118D LEU* 4.3 3.1 - - - +
119D GLU* 3.7 21.3 + - - +
151D LEU* 3.7 31.2 - - + -
897D GLU* 4.7 12.9 + - - +
900D GLU* 4.4 9.3 + - - -
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Residues in contact with LYS 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D ARG* 3.1 31.4 - - - +
112D PRO 2.9 17.0 + - - +
113D VAL* 3.8 12.2 - - - +
115D ARG* 1.3 77.9 - - - +
117D MET* 1.3 77.2 + - - +
119D GLU* 3.5 0.6 + - - -
120D GLU* 2.9 45.4 + - + +
121D CYS* 5.1 2.6 - - - -
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Residues in contact with MET 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D GLU* 3.3 30.5 - - + +
101D ARG* 3.4 27.6 - - - +
102D PHE* 3.7 42.2 - - + +
113D VAL* 2.9 33.6 + - - +
114D VAL 4.4 0.2 - - - +
116D LYS* 1.3 91.5 - - - +
118D LEU* 1.3 59.5 + - - +
119D GLU 3.3 0.7 - - - -
121D CYS* 3.3 39.5 + - - +
124D LEU* 3.5 18.5 - - + +
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Residues in contact with LEU 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D PHE* 3.8 20.6 - - + -
114D VAL* 2.9 24.2 + - + +
115D ARG* 4.4 3.8 - - - +
116D LYS 3.2 0.2 - - - -
117D MET* 1.3 77.1 - - - +
119D GLU* 1.3 58.0 + - - +
121D CYS 5.1 2.7 - - - -
124D LEU* 4.9 1.6 - - + -
126D VAL* 3.8 29.2 - - + -
151D LEU* 3.5 41.7 - - + +
152D LEU* 4.1 9.9 - - + -
155D LYS* 3.2 40.9 + - - +
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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