Contacts of the helix formed by residues 134 - 139 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74D TRP* 4.7 3.4 - - + -
75D LEU* 3.9 17.9 - - + -
78D PHE* 3.5 51.6 - - + +
79D MSE 4.2 6.7 - - + -
130D ARG 3.9 7.0 - - - +
131D LEU* 3.3 27.5 + - + +
132D HIS 4.3 5.0 - - - +
133D SER* 1.3 77.5 - - - +
135D PRO* 1.3 82.1 - - + +
136D VAL* 3.3 6.1 + - - +
138D ASN* 4.0 7.9 - - + +
194D VAL* 3.7 24.8 + - + +
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Residues in contact with PRO 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D PHE* 6.0 0.7 - - + -
133D SER 3.2 10.5 - - - +
134D ILE* 1.3 86.5 - - + +
136D VAL* 1.3 64.0 + - - +
137D CYS* 3.1 16.4 - - - +
138D ASN* 2.9 41.8 + - - +
139D CYS 4.4 0.5 + - - -
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Residues in contact with VAL 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C ASN* 4.4 2.4 + - - -
146C VAL* 5.1 8.7 - - + -
134D ILE 4.1 2.7 - - - +
135D PRO* 1.3 67.6 - - - +
137D CYS* 1.3 59.9 + - - +
138D ASN 3.0 10.4 + - - -
139D CYS 3.1 12.5 + - - +
192D SER* 3.7 13.0 - - - +
193D VAL* 3.6 37.0 - - + -
194D VAL* 4.0 10.3 - - + +
222D ILE* 3.7 32.8 - - + +
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Residues in contact with CYS 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C ASN* 5.8 0.2 - - - +
146C VAL* 3.5 39.3 - - + +
147C PHE* 3.4 27.9 - - - +
150C ALA* 3.6 25.2 - - + +
151C GLN* 5.8 0.2 - - - +
135D PRO* 3.1 21.4 - - - -
136D VAL* 1.3 81.3 - - - +
138D ASN* 1.3 62.0 + - - +
139D CYS 3.4 0.2 - - - -
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Residues in contact with ASN 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C PHE* 3.7 8.2 - - - -
150C ALA* 5.3 4.1 - - - +
74D TRP* 2.9 24.7 + - + -
78D PHE* 3.7 32.5 - - + -
134D ILE* 4.0 4.1 - - + +
135D PRO* 2.9 48.4 + - - +
136D VAL 3.0 1.2 - - - -
137D CYS* 1.3 85.1 - - - +
139D CYS* 1.3 57.2 + - - +
140D PRO* 3.4 4.7 - - - +
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Residues in contact with CYS 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C ASN* 3.0 24.8 + - - -
147C PHE* 3.7 3.1 - - - -
74D TRP* 3.4 32.8 - - + -
136D VAL 3.1 11.0 + - - +
137D CYS 3.4 0.4 - - - -
138D ASN* 1.3 76.9 - - - +
140D PRO* 1.3 63.6 - - - +
141D PHE* 3.4 29.3 + - - -
194D VAL* 3.9 16.2 - - + -
221D GLY* 4.1 14.6 - - - -
222D ILE* 3.8 13.1 - - + +
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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