Contacts of the helix formed by residues 107 - 116 (chain A) in PDB entry 1C06
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 LEU 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A LEU* 3.7 17.3 - - + -
77A HIS* 4.3 9.2 - - + +
103A LYS 5.1 2.7 - - - +
104A SER* 3.6 41.1 - - - +
105A ARG 2.9 3.2 - - - -
106A ASN* 1.3 76.0 - - - +
108A GLN* 1.3 66.9 + - - +
109A VAL* 3.8 17.3 - - + -
110A ILE* 2.7 22.3 + - + -
111A LYS* 2.7 21.9 + - - +
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Residues in contact with GLN 108 (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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106A ASN 3.0 7.2 + - - -
107A LEU* 1.3 70.6 - - - +
109A VAL* 1.3 57.3 + - - +
111A LYS* 4.3 7.4 - - - -
112A GLU* 2.5 58.6 + - + +
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Residues in contact with VAL 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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62A LEU 3.8 0.2 - - - +
63A ALA* 4.2 4.2 - - - -
64A ARG* 4.6 2.9 + - + +
68A GLN* 3.6 39.9 - - + +
72A LEU* 4.6 15.5 - - + -
107A LEU* 3.8 24.9 - - + -
108A GLN* 1.3 76.6 - - - +
110A ILE* 1.3 63.0 + - + +
112A GLU* 3.8 9.7 - - - +
113A ALA* 3.2 24.1 + - - +
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Residues in contact with ILE 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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62A LEU* 3.3 28.3 - - + +
72A LEU* 3.9 21.3 - - + -
77A HIS* 5.8 0.7 - - + -
78A ILE* 5.8 1.3 - - + -
100A VAL* 3.9 14.6 - - + -
104A SER* 3.3 27.1 - - - +
105A ARG* 4.5 1.6 - - - +
107A LEU* 2.7 33.0 + - + +
109A VAL* 1.3 70.0 - - - +
111A LYS* 1.3 55.1 + - - +
112A GLU 2.5 16.2 + - - -
113A ALA* 2.5 14.4 + - - -
114A LEU* 2.8 25.3 + - + +
131A MET* 3.6 26.2 - - + -
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Residues in contact with LYS 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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105A ARG 3.1 23.1 - - - +
106A ASN* 3.6 26.1 + - - +
107A LEU 2.7 21.4 + - - +
108A GLN* 4.0 6.1 - - - +
110A ILE* 1.3 72.2 - - - +
112A GLU* 1.3 50.3 + - - +
114A LEU* 3.9 21.8 - - + -
115A GLU* 2.4 34.0 - - - +
131A MET* 4.4 4.9 - - + -
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Residues in contact with GLU 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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64A ARG* 4.1 32.2 + - + +
108A GLN* 2.5 43.7 + - + +
109A VAL* 3.8 8.9 - - - +
110A ILE 2.5 4.6 + - - -
111A LYS* 1.3 73.4 - - - +
113A ALA* 1.3 62.3 + - - +
114A LEU 3.3 0.4 + - - -
115A GLU* 3.6 14.2 + - - +
116A ALA 3.8 5.5 + - - -
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Residues in contact with ALA 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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61A GLY* 2.8 15.5 - - - +
62A LEU 3.3 3.8 - - - -
63A ALA* 3.0 52.5 - - - +
64A ARG* 3.6 5.2 - - - +
109A VAL 3.2 9.8 + - - +
110A ILE 2.5 10.9 + - - +
112A GLU* 1.3 70.2 - - - +
114A LEU* 1.3 64.4 + - - +
115A GLU 3.1 2.7 - - - -
116A ALA* 2.9 26.9 + - + +
117A ASN 3.8 0.3 + - - -
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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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60A LEU 5.9 0.2 - - - -
61A GLY* 3.1 15.2 + - - +
62A LEU* 3.7 24.0 - - + -
110A ILE* 2.8 22.6 + - + +
111A LYS* 3.9 21.1 - - + +
112A GLU 3.3 0.4 - - - -
113A ALA* 1.3 78.1 - - - +
115A GLU* 1.3 75.5 + - - +
117A ASN* 3.6 15.8 + - - +
126A PHE* 4.4 14.6 - - + -
128A PRO* 5.6 10.5 - - + +
131A MET* 4.2 22.0 - - + -
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Residues in contact with GLU 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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64A ARG* 6.1 1.1 - - - +
111A LYS 2.4 26.2 - - - +
112A GLU* 3.6 9.3 + - - +
113A ALA 3.1 0.4 - - - -
114A LEU* 1.3 88.6 - - - +
116A ALA* 1.3 53.5 + - - +
117A ASN* 2.6 21.3 + - - +
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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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61A GLY* 4.8 3.3 - - - -
63A ALA 5.7 0.4 - - - +
64A ARG* 3.0 52.2 - - - +
112A GLU 3.8 1.2 + - - -
113A ALA* 2.9 16.9 + - + +
115A GLU* 1.3 76.2 - - - +
117A ASN* 1.3 49.9 + - - -
118A ASN* 2.6 28.1 + - - +
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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