Contacts of the helix formed by residues 134 - 140 (chain D) in PDB entry 3HU1
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 TYR 134 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126D ILE 5.9 2.2 - - - -
127D THR 5.4 3.8 - - - -
129D ASN 5.1 0.4 - - - -
130D LEU* 3.3 38.3 + - + +
132D GLU 3.5 0.2 - - - -
133D VAL* 1.3 97.3 - - + +
135D LEU* 1.3 66.0 + - - +
136D LYS 3.6 1.1 - - - -
137D PRO* 3.3 13.6 - - - +
138D TYR 3.4 3.8 + - - -
154D VAL* 3.3 33.2 - - + +
155D ARG 4.2 1.3 - - - -
156D GLY* 3.6 32.1 - - - -
158D MET* 3.3 33.6 - - + +
159D ARG* 3.6 18.3 + - - +
161D VAL* 3.7 23.9 - - + +
163D PHE* 4.1 18.4 - + + -
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Residues in contact with LEU 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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116D VAL* 3.7 26.5 - - + -
130D LEU 3.3 15.5 + - - +
131D PHE* 3.3 15.9 + - + +
134D TYR* 1.3 75.8 - - - +
136D LYS* 1.3 59.6 - - - +
138D TYR* 3.2 4.8 + - - +
139D PHE* 3.0 47.1 + - + -
152D PHE* 4.0 23.1 - - + -
154D VAL* 4.8 2.0 - - + -
163D PHE* 3.9 42.2 - - + -
182D ILE* 4.4 6.7 - - + -
184D CYS* 4.1 20.6 - - - -
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Residues in contact with LYS 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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131D PHE* 2.8 57.5 + - + +
132D GLU* 4.5 19.9 + - - +
135D LEU* 1.3 72.3 - - - +
137D PRO* 1.4 61.2 - - + +
139D PHE* 3.3 2.8 + - - -
140D LEU* 2.9 64.4 + - + +
182D ILE* 5.5 1.3 - - + -
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Residues in contact with PRO 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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132D GLU 3.5 20.6 - - - +
133D VAL 3.3 20.0 - - - +
134D TYR* 3.3 13.7 - - - +
136D LYS* 1.4 89.5 - - + +
138D TYR* 1.3 58.6 + - - +
140D LEU* 4.5 10.6 + - + +
154D VAL* 5.9 0.2 - - + -
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Residues in contact with TYR 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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35D ASP* 4.9 0.9 - - - -
36D ASN* 3.2 41.6 + - - +
37D SER* 4.6 1.0 + - - -
134D TYR 3.4 13.2 + - - +
135D LEU* 3.2 8.6 + - + +
137D PRO* 1.3 80.8 - - - +
139D PHE* 1.3 90.0 + + - +
140D LEU 5.1 0.2 - - - +
142D ALA* 4.1 4.9 - - - +
144D ARG* 3.1 61.3 + - - +
146D ILE* 5.5 4.0 - - + +
152D PHE* 3.5 33.0 - + - +
153D LEU 4.1 2.0 - - - -
154D VAL* 3.7 26.7 - - + +
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Residues in contact with PHE 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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114D ILE* 4.5 15.9 - - + -
116D VAL* 5.5 0.2 - - + -
135D LEU* 3.0 44.9 + - + +
136D LYS* 4.4 1.3 - - - +
138D TYR* 1.3 107.4 - + - +
140D LEU* 1.3 67.5 - - - +
141D GLU 3.2 1.2 + - - -
142D ALA* 3.1 16.9 + - - +
143D TYR 4.1 3.8 + - - -
144D ARG* 3.7 22.2 - - + -
146D ILE* 4.2 11.9 - - + -
152D PHE* 4.0 11.7 - + - -
176D VAL* 3.6 50.7 - - + +
177D ALA 6.1 0.3 - - - -
178D PRO* 5.9 0.7 - - - +
182D ILE* 4.1 22.2 - - + -
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Residues in contact with LEU 140 (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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136D LYS* 2.9 47.8 + - + +
137D PRO* 4.5 8.3 + - + +
138D TYR 3.8 0.6 - - - -
139D PHE* 1.3 74.5 - - - +
141D GLU* 1.3 76.9 + - + +
142D ALA* 2.8 15.8 + - - +
178D PRO* 5.9 8.3 - - + -
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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