Contacts of the helix formed by residues 134 - 139 (chain C) in PDB entry 4GKH
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 ILE 134 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C TRP* 4.6 4.3 - - + -
75C LEU* 3.9 19.7 - - + -
78C PHE* 3.6 48.2 - - + +
79C MSE 4.0 8.3 - - + -
130C ARG 4.1 5.6 - - - +
131C LEU* 3.2 28.5 + - + +
132C HIS 4.2 4.5 - - - +
133C SER* 1.3 76.4 + - - +
135C PRO* 1.3 81.2 - - + +
136C VAL* 3.3 3.5 + - - +
138C ASN* 4.2 10.3 - - + +
194C VAL* 3.4 26.8 + - + +
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Residues in contact with PRO 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C PHE* 5.9 1.1 - - + -
133C SER 3.1 9.8 - - - +
134C ILE* 1.3 87.6 - - + +
136C VAL* 1.3 65.0 + - - +
137C CYS* 3.9 14.8 - - - +
138C ASN* 3.1 40.9 + - - +
194C VAL* 4.4 0.3 - - - +
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Residues in contact with VAL 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C ILE 4.1 2.5 - - - +
135C PRO* 1.3 68.4 - - - +
137C CYS* 1.3 64.4 + - - +
138C ASN 3.0 5.8 - - - -
139C CYS 3.0 15.5 + - - +
192C SER* 3.8 28.0 - - - +
193C VAL* 3.9 17.3 - - - -
194C VAL* 4.0 13.9 - - - +
222C ILE* 3.8 32.6 - - + +
142D ASN* 4.4 2.8 + - - -
146D VAL* 5.1 8.3 - - + -
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Residues in contact with CYS 137 (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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135C PRO* 3.1 20.3 - - - -
136C VAL* 1.3 81.2 - - - +
138C ASN* 1.3 65.3 + - - +
139C CYS 3.4 0.2 - - - -
146D VAL* 3.6 36.6 - - + +
147D PHE* 3.1 31.7 - - - +
150D ALA* 4.0 19.7 - - + +
151D GLN* 6.0 0.2 - - - +
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Residues in contact with ASN 138 (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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74C TRP* 2.9 27.4 + - + -
78C PHE* 3.7 33.7 - - + -
134C ILE* 4.2 4.3 - - + +
135C PRO* 3.1 45.7 + - - +
136C VAL 3.0 0.8 - - - -
137C CYS* 1.3 84.6 - - - +
139C CYS* 1.3 56.6 + - - +
140C PRO* 3.5 4.0 - - - +
147D PHE* 3.7 7.9 - - - -
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Residues in contact with CYS 139 (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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74C TRP* 3.5 31.4 - - + -
136C VAL 3.0 10.7 + - - +
137C CYS 3.4 0.8 - - - -
138C ASN* 1.3 77.8 - - - +
140C PRO* 1.3 62.7 - - - +
141C PHE* 3.3 29.6 + - - -
194C VAL* 4.1 11.9 - - + -
221C GLY* 4.1 14.1 - - - -
222C ILE* 3.6 17.2 - - + +
142D ASN* 2.8 26.5 + - - -
147D PHE* 3.5 4.4 - - - -
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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