Contacts of the helix formed by residues 132 - 137 (chain F) in PDB entry 6C3P
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 PHE 132 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B GLN* 3.5 20.9 - - + -
53B GLY* 2.9 41.5 - - - -
54B ARG 2.9 23.3 - - - -
55B PHE* 3.1 31.0 - - + +
56B LEU* 5.4 1.8 - - + -
58B ASP* 4.2 5.2 - - - -
127F ILE* 4.4 4.6 - - + +
130F SER* 3.3 13.2 + - - -
131F ASN* 1.3 78.1 - - - +
133F PRO* 1.3 51.7 - - - +
134F LYS* 2.5 6.5 + - + +
135F LEU* 2.2 50.3 + - + -
136F LEU 4.2 0.2 - - - -
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Residues in contact with PRO 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131F ASN* 3.1 25.8 - - + +
132F PHE* 1.3 79.9 - - - +
134F LYS* 1.3 56.7 + - - +
135F LEU 3.1 0.4 - - - -
136F LEU* 3.3 18.2 - - + +
137F ILE* 2.9 19.2 + - - +
189F VAL* 6.2 3.8 - - + -
193F ARG* 5.1 7.0 - - + -
195F TYR* 2.5 53.8 + - + +
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Residues in contact with LYS 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LEU* 6.1 4.3 - - + -
132F PHE* 2.5 7.4 + - + +
133F PRO* 1.3 74.2 - - - +
135F LEU* 1.3 57.7 + - - +
137F ILE* 3.0 30.0 - - + +
138F ALA 4.5 0.3 + - - -
195F TYR* 3.1 21.8 - - + -
196F ILE* 5.9 1.1 - - - +
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Residues in contact with LEU 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B PHE 5.6 0.2 - - - +
56B LEU* 4.9 15.3 - - + +
46F ILE* 6.3 0.4 - - + -
123F TYR* 3.5 22.7 + - - +
127F ILE* 5.5 7.2 - - + -
132F PHE* 2.2 43.3 + - + +
134F LYS* 1.3 69.2 - - - +
136F LEU* 1.3 60.4 + - - +
138F ALA* 3.6 16.1 + - - +
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Residues in contact with LEU 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F TYR* 5.1 3.6 - - + -
124F TYR* 5.2 14.1 - - + -
127F ILE* 4.8 14.8 - - + +
131F ASN* 6.0 1.1 - - + -
132F PHE 3.5 1.2 + - - -
133F PRO* 3.0 25.7 + - + +
135F LEU* 1.3 76.1 - - - +
137F ILE* 1.3 56.2 + - - +
138F ALA 3.0 5.4 - - - -
139F LEU* 2.8 39.2 + - + +
186F GLU* 4.4 5.9 - - - +
195F TYR* 4.9 0.9 - - - +
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Residues in contact with ILE 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F PRO 2.9 6.4 + - - +
134F LYS* 3.0 30.7 - - + +
136F LEU* 1.3 71.9 - - - +
138F ALA* 1.3 65.1 + - - +
139F LEU 3.0 0.9 - - - -
140F LEU* 2.8 44.3 + - + +
141F VAL* 3.2 14.9 + - + +
186F GLU* 3.9 13.2 - - - +
190F ILE* 5.8 5.2 - - + -
195F TYR* 2.9 30.3 - - + +
196F ILE* 5.4 7.4 - - + -
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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