Contacts of the helix formed by residues 106 - 111 (chain C) in PDB entry 3G1Q
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 MET 106 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C TYR* 2.9 28.6 + - + +
105C PHE* 1.3 112.1 - - + +
107C VAL* 1.4 58.2 + - - +
108C PRO* 3.2 4.3 - - - -
109C VAL* 2.9 28.8 + - + -
110C PHE* 3.0 55.3 + - + -
208C LEU* 4.0 26.5 - - + -
290C PHE* 4.1 15.9 - - + -
460C MET* 5.5 3.1 - - + -
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Residues in contact with VAL 107 (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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103C TYR 3.7 2.6 + - - +
104C SER* 3.2 29.1 + - - +
106C MET* 1.4 75.7 - - - +
108C PRO* 1.4 62.3 - - + +
110C PHE* 5.1 2.7 - - - -
111C GLY* 2.7 34.1 + - - +
112C GLU* 3.6 46.9 + - + +
113C GLY 5.0 0.2 - - - +
117C ALA* 4.0 23.6 - - + -
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Residues in contact with PRO 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C SER 4.2 1.6 - - - +
105C PHE 3.5 15.7 - - - +
106C MET 3.3 5.2 - - - -
107C VAL* 1.4 94.3 - - + +
109C VAL* 1.4 57.4 + - + +
111C GLY* 4.4 0.4 - - - -
112C GLU* 6.3 0.7 - - + -
207C SER* 4.3 12.3 - - - +
208C LEU* 5.2 1.6 - - + -
219C LEU* 6.1 1.6 - - + -
226C SER* 5.7 8.3 - - - +
229C CYS* 3.4 28.9 - - + +
230C HIS* 5.8 0.9 - - - -
233C ARG* 3.7 15.9 - - - +
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Residues in contact with VAL 109 (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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106C MET* 2.9 20.0 + - + +
108C PRO* 1.4 76.2 - - - +
110C PHE* 1.3 71.6 + - + +
111C GLY 3.3 0.9 - - - -
204C MET* 3.4 55.1 - - + +
208C LEU* 4.0 15.9 - - + -
229C CYS* 3.9 5.2 - - - -
233C ARG* 3.0 20.4 + - - -
286C VAL* 3.4 27.1 - - + +
290C PHE* 3.9 19.3 - - + -
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Residues in contact with PHE 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C TYR* 4.4 3.6 - + + -
106C MET* 3.0 60.6 + - + +
107C VAL* 4.7 2.2 - - + +
109C VAL* 1.3 84.2 - - + +
111C GLY* 1.3 60.5 + - - +
114C VAL* 3.4 28.8 - - + +
115C ALA* 4.3 9.6 - - + -
116C TYR* 3.6 39.0 - + - -
233C ARG* 3.0 15.4 + - - -
283C GLY* 3.2 18.2 - - - +
287C ALA* 3.6 37.7 - - + -
290C PHE* 4.9 2.7 - - + -
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Residues in contact with GLY 111 (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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107C VAL* 2.7 27.9 + - - +
108C PRO 5.0 0.4 - - - -
109C VAL 3.3 1.6 - - - -
110C PHE* 1.3 77.5 - - - +
112C GLU* 1.3 69.0 + - - -
113C GLY 3.3 0.5 + - - -
114C VAL* 3.2 16.3 + - - +
117C ALA* 4.6 1.2 - - - +
233C ARG* 3.9 9.4 - - - -
279C HIS* 3.7 16.2 - - - -
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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