Contacts of the helix formed by residues 102 - 106 (chain B) in PDB entry 1CD9
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 ASP 102 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LYS* 2.9 32.8 + - - +
78B TYR* 3.1 38.4 + - - -
79B GLN 3.5 13.0 - - - +
80B TYR* 4.4 7.1 - - + +
101B LEU* 1.3 77.4 - - - +
103B PRO* 1.3 73.2 - - - +
104B MET* 3.1 15.5 + - - +
105B ASP* 2.7 38.8 + - - +
106B VAL 3.9 1.7 + - - -
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Residues in contact with PRO 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B MET* 3.3 27.5 - - - +
22B LEU* 4.4 6.1 - - + -
75B LEU* 4.3 12.8 - - + -
76B LEU 4.2 7.4 - - - +
77B LEU* 3.6 28.0 - - + -
79B GLN 3.7 10.3 - - - +
81B MET* 3.8 26.0 - - - -
101B LEU* 3.6 13.6 - - + +
102B ASP* 1.3 87.6 - - - +
104B MET* 1.3 60.2 + - - +
105B ASP 3.1 1.4 + - - -
106B VAL* 3.2 21.6 + - + +
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Residues in contact with MET 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU* 4.3 2.7 - - - +
24A LYS* 5.0 3.8 - - - +
15B MET* 4.4 8.5 - - - -
17B LEU* 4.9 3.4 - - + -
77B LEU* 3.9 34.1 - - + -
78B TYR* 3.4 51.1 - - + +
102B ASP* 2.9 12.4 + - - +
103B PRO* 1.3 75.4 - - - +
105B ASP* 1.3 59.4 + - - +
106B VAL 3.3 0.4 - - - -
107B VAL* 3.6 30.8 + - + +
143B TYR* 2.8 31.6 - - + +
144B MET* 4.9 1.3 - - + -
193B ARG* 3.0 25.1 + - - +
197B PRO 4.2 0.5 - - - +
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Residues in contact with ASP 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LYS* 4.2 13.5 + - - -
80B TYR* 4.3 15.8 + - - -
101B LEU* 5.4 1.9 - - + -
102B ASP* 2.7 38.1 + - + +
104B MET* 1.3 71.4 - - - +
106B VAL* 1.3 66.7 + - + +
107B VAL 3.6 0.9 - - - -
193B ARG* 3.1 17.3 + - - -
197B PRO* 3.3 53.6 - - + +
198B GLY* 3.9 5.2 + - - -
199B PHE* 4.7 2.4 - - - -
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Residues in contact with VAL 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B CYS 3.5 24.9 - - - +
14B LEU* 3.3 7.4 - - - +
15B MET 2.8 25.4 + - - +
22B LEU* 4.1 13.2 - - + -
101B LEU* 4.4 21.1 - - + -
102B ASP 4.3 2.7 - - - +
103B PRO* 3.2 17.0 + - + +
105B ASP* 1.3 89.0 - - + +
107B VAL* 1.3 64.4 + - - +
108B LYS 3.4 0.2 + - - -
199B PHE* 3.9 24.0 - - + -
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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