Contacts of the helix formed by residues 135 - 147 (chain D) in PDB entry 3KHU
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 ARG 135 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106D LEU* 5.7 1.3 - - - -
134D VAL* 1.3 81.1 - - + +
136D ALA* 1.3 64.8 + - - +
137D ALA 3.3 2.2 - - - -
138D GLU* 3.2 33.9 + - - +
139D SER* 3.2 15.1 + - - +
214D TRP* 4.7 8.9 - - - +
217D GLU* 3.0 10.9 + - - -
287D LEU* 6.1 1.1 - - + -
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Residues in contact with ALA 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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106D LEU* 4.2 23.1 - - + -
109D ILE* 5.2 2.5 - - + +
128D GLU* 3.0 19.3 - - - +
132D VAL* 3.6 18.6 - - + -
133D PRO* 3.1 19.8 + - + +
134D VAL 3.4 0.8 + - - -
135D ARG* 1.3 76.7 - - - +
137D ALA* 1.3 61.0 + - - +
139D SER* 2.9 20.1 + - - -
140D ILE* 3.1 16.9 + - + +
217D GLU* 3.6 1.7 + - - +
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Residues in contact with ALA 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D GLU* 3.0 12.9 + - - +
135D ARG 3.3 0.4 - - - -
136D ALA* 1.3 74.8 - - - +
138D GLU* 1.3 57.1 + - - +
140D ILE* 3.4 8.4 + - - +
141D ARG* 2.9 29.6 + - - +
156D VAL* 4.0 17.1 - - + +
157D LEU 5.5 0.4 - - - +
213D THR* 3.4 33.2 - - + -
217D GLU* 2.9 15.3 + - - +
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Residues in contact with GLU 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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135D ARG* 3.2 28.6 + - - +
136D ALA 3.1 0.2 - - - -
137D ALA* 1.3 78.7 - - - +
139D SER* 1.3 58.8 + - - +
141D ARG* 3.5 7.7 + - - +
142D ARG* 3.0 42.6 + - + +
214D TRP* 4.4 26.5 + - + +
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Residues in contact with SER 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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106D LEU* 4.2 15.3 - - - +
109D ILE* 6.1 2.0 - - - -
135D ARG* 3.2 9.3 + - - +
136D ALA* 2.9 12.4 + - - -
138D GLU* 1.3 77.4 + - - +
140D ILE* 1.3 66.6 + - - +
142D ARG* 3.1 5.6 + - - +
143D ILE* 3.1 29.4 + - - +
323F PHE* 3.4 39.0 - - - +
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Residues in contact with ILE 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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87D ILE* 4.2 12.8 - - + -
109D ILE* 3.8 29.4 - - + -
113D ALA* 4.3 17.3 - - + -
126D VAL* 4.7 6.3 - - + -
128D GLU* 3.6 38.1 - - + +
136D ALA 3.1 8.1 + - - +
137D ALA* 3.6 7.4 - - - +
139D SER* 1.3 74.8 - - - +
141D ARG* 1.3 64.7 + - - +
143D ILE* 3.2 5.2 + - + +
144D PHE* 3.0 55.0 + - + -
156D VAL* 4.0 13.5 - - + -
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Residues in contact with ARG 141 (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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137D ALA 2.9 17.3 + - - +
138D GLU* 3.6 9.0 - - + +
140D ILE* 1.3 79.0 - - - +
142D ARG* 1.3 57.2 + - + +
144D PHE* 3.4 24.3 + - - +
145D ASP* 2.9 67.2 + - - +
154D LEU* 2.8 34.1 + - - +
155D GLN* 4.1 10.1 + - - +
156D VAL* 3.9 23.9 - - + +
183D ASP* 5.3 8.2 + - - -
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Residues in contact with ARG 142 (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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138D GLU* 3.0 34.6 + - + +
139D SER* 3.1 6.4 + - - +
141D ARG* 1.3 74.4 - - + +
143D ILE* 1.3 64.1 + - - +
145D ASP* 3.4 7.4 + - + +
146D ALA* 3.0 26.3 + - - +
323F PHE* 4.5 20.4 - - + -
435F PRO* 4.9 6.4 - - + +
458F GLN* 6.0 5.8 - - - +
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Residues in contact with ILE 143 (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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110D GLU* 3.7 25.6 - - + +
113D ALA* 3.8 29.4 - - + +
114D ARG* 3.9 32.5 - - + +
117D VAL* 4.4 3.8 - - + -
139D SER* 3.1 15.6 + - - +
140D ILE* 3.2 6.3 + - + +
142D ARG* 1.3 75.9 - - - +
144D PHE* 1.3 62.1 + - + +
146D ALA* 3.3 2.5 + - - -
147D ASN* 2.8 43.3 + - - +
323F PHE* 3.7 31.9 - - + -
435F PRO* 4.8 3.4 - - + -
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Residues in contact with PHE 144 (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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113D ALA* 3.3 36.1 - - + -
116D ILE* 4.2 9.2 - - + -
117D VAL* 4.1 8.7 - - + +
126D VAL* 3.9 22.9 - - + -
140D ILE* 3.0 35.8 + - + -
141D ARG* 3.6 21.3 - - - +
143D ILE* 1.3 78.9 - - + +
145D ASP* 1.3 62.5 + - - +
147D ASN* 3.2 21.7 + - - +
148D THR* 3.5 6.6 + - - -
152D LEU* 5.7 1.8 - - + +
154D LEU* 3.6 44.6 - - + -
156D VAL* 3.8 22.2 - - + -
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Residues in contact with ASP 145 (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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141D ARG* 2.9 57.2 + - - +
142D ARG* 3.9 8.0 - - + +
144D PHE* 1.3 74.1 - - - +
146D ALA* 1.3 60.5 + - - +
147D ASN 3.6 0.3 + - - -
148D THR* 4.0 14.6 - - - +
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Residues in contact with ALA 146 (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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142D ARG 3.0 17.8 + - - +
143D ILE 3.9 3.6 - - - +
145D ASP* 1.3 75.7 - - - +
147D ASN* 1.3 62.4 + - - +
148D THR* 3.6 2.4 + - - -
434F LYS* 3.9 11.9 - - + +
435F PRO* 3.8 38.8 - - + -
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Residues in contact with ASN 147 (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 ARG* 4.1 4.5 + - - +
117D VAL* 3.0 37.9 - - + +
143D ILE* 2.8 36.6 + - - +
144D PHE 3.2 4.2 + - - -
146D ALA* 1.3 81.3 - - - +
148D THR* 1.3 63.9 + - - +
149D LYS* 3.9 3.5 + - - +
152D LEU* 4.4 0.5 - - - +
434F LYS* 3.1 44.3 + - - +
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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