Contacts of the helix formed by residues 111 - 117 (chain C) in PDB entry 5F1B
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 111 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C GLN* 2.7 30.0 + - - -
109C ILE* 3.2 15.0 + - - -
110C LEU* 1.3 76.1 - - - +
112C VAL* 1.3 61.1 + - - +
113C LEU* 3.1 18.1 + - - +
114C ASN* 2.9 26.5 + - - +
115C TYR 4.2 0.7 + - - -
118C ASN* 5.0 0.2 - - - -
169C VAL* 3.6 9.3 - - - +
174C VAL* 3.3 13.7 - - - +
190C VAL 4.1 3.4 - - - -
191C ILE* 4.0 10.5 - - - +
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Residues in contact with VAL 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C LEU* 4.6 4.9 - - + -
68C LEU* 4.0 10.1 - - + -
111C SER* 1.3 74.3 + - - +
113C LEU* 1.3 78.9 + - + +
115C TYR* 3.2 35.3 + - + +
116C PHE* 3.7 9.9 - - + -
141C PHE* 3.7 32.8 - - + -
174C VAL* 3.8 20.7 + - + +
175C LEU* 4.3 10.1 - - + -
189C LEU* 3.8 31.6 - - + -
190C VAL 4.9 0.6 + - - -
191C ILE* 5.7 1.1 - - + +
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Residues in contact with LEU 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C LEU* 3.6 31.2 - - + +
71C VAL* 3.6 32.8 - - + -
72C LEU* 3.8 26.7 - - + +
75C GLN* 4.0 7.2 - - - +
111C SER* 3.0 17.3 + - - +
112C VAL* 1.3 94.1 - - + +
114C ASN* 1.3 56.6 + - - +
115C TYR 3.2 0.2 - - - -
116C PHE* 3.0 20.4 + - + +
118C ASN* 3.0 30.3 + - - +
123C LEU* 4.2 21.1 - - + -
191C ILE* 4.9 0.2 - - + -
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Residues in contact with ASN 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C ILE* 2.6 37.7 + - - +
111C SER* 2.9 16.5 + - - +
113C LEU* 1.3 75.1 - - - +
115C TYR* 1.3 56.2 + - - +
116C PHE 2.9 5.6 - - - -
117C GLN* 2.9 22.5 + - - +
118C ASN* 3.1 25.6 + - - +
161C CYS 3.8 1.2 - - - +
162C LEU 3.6 1.4 - - - +
163C GLY* 3.4 18.9 - - - -
164C THR* 2.9 21.7 + - - +
165C PHE* 3.6 18.2 - - - -
169C VAL* 3.8 13.5 - - + -
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Residues in contact with TYR 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C SER 4.2 0.2 + - - -
112C VAL* 3.2 40.3 + - + +
113C LEU 3.2 1.0 - - - -
114C ASN* 1.3 77.9 - - - +
116C PHE* 1.3 65.2 - + + +
117C GLN* 3.0 11.2 - - - +
140C HIS* 2.7 28.6 + - + +
141C PHE* 4.7 7.9 - + - -
144C CYS* 3.7 40.6 - - + -
145C VAL* 3.9 18.0 - - + +
148C PRO* 4.5 4.3 - - + -
160C PRO 3.3 1.6 - - - +
161C CYS* 3.6 18.1 - - - -
169C VAL* 2.4 46.2 + - + +
170C PHE 3.8 0.2 - - - -
171C PRO* 3.3 26.0 - - + +
174C VAL* 4.7 4.5 - - + -
175C LEU* 5.8 0.2 - - + -
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Residues in contact with PHE 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C LEU* 5.6 4.5 - - + -
112C VAL* 3.7 24.9 - - + -
113C LEU* 3.0 14.2 + - + +
114C ASN 2.9 0.6 - - - -
115C TYR* 1.3 86.8 - + + +
117C GLN* 1.3 72.6 + - - +
118C ASN 3.1 2.0 + - - -
119C SER* 3.2 12.9 + - - +
122C VAL* 3.4 31.1 - - + +
123C LEU* 3.6 38.4 - - + +
137C TYR* 3.5 53.4 - + + -
140C HIS* 3.7 23.3 - + + -
141C PHE* 4.5 8.5 - + + -
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Residues in contact with GLN 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C ASN* 2.9 20.6 + - - -
115C TYR 3.0 19.6 + - - +
116C PHE* 1.3 87.1 + - - +
118C ASN* 1.3 69.8 + - - +
119C SER* 3.1 8.3 + - - -
122C VAL* 3.6 22.0 - - + +
159C ASP* 5.6 0.2 - - - -
160C PRO* 3.1 38.0 + - + +
161C CYS 4.2 0.2 - - - -
162C LEU 3.3 23.5 - - - +
163C GLY 5.0 0.2 - - - -
164C THR* 4.7 17.6 + - - +
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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