Contacts of the helix formed by residues 131 - 140 (chain D) in PDB entry 7KHI
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 PRO 131 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129D ASP 4.3 4.5 - - - +
130D MET* 1.3 90.3 - - + +
132D LEU* 1.3 66.3 + - - +
133D ARG* 4.5 7.0 - - + +
134D ASP* 3.3 27.2 + - + +
135D ILE* 3.3 11.6 + - - +
85F SER* 5.9 6.1 - - - +
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Residues in contact with LEU 132 (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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117D LEU* 3.8 25.6 - - + +
118D LYS* 5.2 13.5 - - + +
119D SER 5.9 0.4 - - - +
120D LEU 5.6 1.8 - - - +
122D SER* 3.4 31.6 - - - +
125D GLY* 6.0 0.2 - - - -
130D MET 3.7 0.6 + - - -
131D PRO* 1.3 73.9 - - - +
133D ARG* 1.3 66.2 + - + +
135D ILE* 3.1 13.9 + - + -
136D GLU* 2.9 42.2 + - + +
78F GLU* 5.0 7.0 - - - +
82F GLN* 4.6 26.6 - - + +
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Residues in contact with ARG 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D LYS* 6.2 0.2 - - - +
131D PRO* 3.4 4.4 - - + +
132D LEU* 1.3 79.3 - - + +
134D ASP* 1.3 57.8 + - - +
136D GLU* 3.4 30.6 + - - +
137D ARG* 2.9 37.2 + - - +
140D TYR* 5.9 4.0 - - - -
82F GLN* 5.0 15.2 - - + +
85F SER* 5.5 4.5 - - - -
86F SER* 4.0 35.2 - - - +
91F ILE* 4.3 28.0 - - + +
92F GLY 5.4 0.8 + - - -
93F ARG* 3.4 45.1 - - - +
95F THR* 5.2 5.3 - - - +
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Residues in contact with ASP 134 (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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130D MET* 3.3 23.8 - - + +
131D PRO* 3.3 30.4 + - + +
132D LEU 3.1 0.4 - - - -
133D ARG* 1.3 79.3 - - - +
135D ILE* 1.3 63.1 + - - +
137D ARG* 3.2 7.6 + - - +
138D VAL* 2.9 24.1 + - - +
157D GLN 5.3 2.5 - - - +
159D ILE* 2.9 50.2 - - - +
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Residues in contact with ILE 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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117D LEU* 4.0 25.1 - - + -
122D SER* 4.6 1.3 - - - +
124D ILE* 4.5 5.6 - - + -
125D GLY* 3.6 35.9 - - - +
128D LEU* 5.7 2.2 - - + -
130D MET* 3.7 20.2 - - + +
131D PRO 3.3 15.3 - - - +
132D LEU* 3.1 17.9 + - + +
134D ASP* 1.3 75.9 - - - +
136D GLU* 1.3 63.6 + - - +
138D VAL* 3.0 7.3 + - - +
139D LEU* 2.9 36.0 + - + +
185D ILE* 4.0 27.6 - - + -
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Residues in contact with GLU 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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117D LEU* 5.3 5.4 - - - +
118D LYS* 3.4 18.7 - - - +
132D LEU* 2.9 29.8 + - + +
133D ARG* 3.5 37.0 - - - +
135D ILE* 1.3 79.6 - - - +
137D ARG* 1.3 63.2 + - - +
138D VAL 3.1 0.3 + - - -
139D LEU* 3.2 9.5 + - - +
140D TYR* 3.1 64.4 + - + -
312D ARG* 3.4 21.7 + - - -
95F THR* 6.5 0.4 - - - -
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Residues in contact with ARG 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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133D ARG* 2.9 23.3 + - - +
134D ASP* 3.2 7.2 + - - +
136D GLU* 1.3 76.7 - - - +
138D VAL* 1.3 62.0 + - - +
140D TYR* 5.0 0.9 - - - -
142D GLU* 3.0 60.1 + - + +
143D SER* 3.0 33.1 + - - +
159D ILE* 5.2 11.2 - - + +
91F ILE* 3.4 48.5 - - - +
92F GLY 5.1 4.8 + - - -
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Residues in contact with VAL 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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130D MET* 5.1 0.7 - - + -
134D ASP* 2.9 23.3 + - - +
135D ILE* 3.0 11.4 + - - +
137D ARG* 1.3 78.6 - - - +
139D LEU* 1.3 65.0 + - - +
141D PHE 3.2 9.4 + - - -
143D SER* 3.8 16.4 - - - +
145D VAL* 3.4 37.0 - - + -
159D ILE* 4.5 4.0 - - + -
179D LYS 5.6 0.2 - - - +
180D MET* 3.7 5.8 - - - +
181D GLY 3.3 28.1 + - - +
184D ALA* 5.0 0.7 - - + -
185D ILE* 3.6 30.3 - - + -
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Residues in contact with LEU 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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112D ALA* 4.4 9.0 - - + -
117D LEU* 3.6 32.1 - - + -
135D ILE* 2.9 27.5 + - + +
136D GLU* 3.2 14.3 + - - +
138D VAL* 1.3 76.7 - - - +
140D TYR* 1.3 71.1 + - + +
141D PHE* 3.0 27.9 - - - -
181D GLY* 4.1 6.3 - - - -
182D ALA* 3.7 25.1 + - + +
185D ILE* 3.6 30.7 - - + -
297D ARG* 5.1 0.5 - - - +
300D GLN* 5.2 12.0 - - + +
312D ARG* 5.8 1.3 - - - +
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Residues in contact with TYR 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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133D ARG* 5.9 3.8 - - - -
136D GLU* 3.1 37.3 + - + +
137D ARG* 5.0 0.7 - - - -
138D VAL 3.3 0.4 - - - -
139D LEU* 1.3 85.9 - - + +
141D PHE* 1.3 57.7 + - - +
142D GLU* 2.7 30.3 - - - +
297D ARG* 2.4 41.8 + - + +
300D GLN* 5.0 15.0 - - + -
301D GLU* 5.5 2.9 + - - -
312D ARG* 2.5 44.7 + - - -
94F THR 5.0 2.9 - - - -
95F THR* 4.7 22.6 - - + -
100F MET* 4.3 19.7 - - + -
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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