Contacts of the helix formed by residues 141 - 153 (chain B) in PDB entry 6IEH
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 ASP 141 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B ILE 3.8 3.7 + - - +
140B LEU* 1.3 79.1 - - - +
142B ALA* 1.3 66.4 + - - +
143B PHE* 3.2 26.7 - - + -
144B GLN* 3.0 13.4 + - + +
145B ARG* 3.0 22.7 + - - +
165B ALA 4.4 0.5 - - - +
311B TYR* 3.1 34.9 + - + -
527B ARG* 4.0 17.0 + - - -
1102B ATP 4.5 4.1 + - - -
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Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B VAL* 4.8 14.6 - - + -
108B GLU* 4.3 24.5 - - + +
110B CYS* 4.5 10.5 - - + -
141B ASP* 1.3 74.2 - - - +
143B PHE* 1.3 61.9 + - - +
145B ARG* 3.4 12.1 + - - +
146B GLU* 3.2 27.1 + - + +
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Residues in contact with PHE 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B CYS* 3.8 22.8 - - + +
141B ASP* 3.8 18.4 - - + -
142B ALA* 1.3 80.7 - - - +
144B GLN* 1.3 85.7 + - + +
146B GLU* 3.4 2.3 + - - +
147B ALA* 3.3 20.4 + - - +
159B VAL* 4.1 22.4 - - + -
161B ALA* 4.1 12.8 - - + -
165B ALA* 3.7 38.1 - - + -
166B GLY 4.0 9.6 - - - -
167B LYS* 4.5 1.1 - - - -
170B CYS* 5.4 1.3 - - - -
307B ILE* 4.1 9.9 - - + +
309B THR* 3.8 30.5 - - + +
311B TYR* 4.2 13.7 - + + -
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Residues in contact with GLN 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B LEU* 3.9 11.2 - - + +
141B ASP* 3.0 22.3 + - - +
143B PHE* 1.3 98.2 - - + +
145B ARG* 1.3 63.6 + - - +
146B GLU 3.2 0.2 + - - -
147B ALA* 3.3 2.1 + - - +
148B ILE* 3.0 26.8 + - - +
165B ALA 4.9 0.2 - - - -
166B GLY* 2.3 37.3 + - - -
169B VAL* 2.6 36.5 - - + +
170B CYS* 4.5 8.6 - - - -
1102B ATP 3.3 30.4 + - - -
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Residues in contact with ARG 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ILE* 3.7 16.6 - - - +
140B LEU* 2.6 63.1 + - + +
141B ASP 3.0 11.8 + - - +
142B ALA* 3.7 11.7 - - - +
144B GLN* 1.3 78.3 - - - +
146B GLU* 1.3 65.2 + - + +
148B ILE* 3.5 8.3 + - + +
149B GLN* 3.3 21.1 + - - +
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Residues in contact with GLU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B VAL* 5.0 1.9 - - - +
105B GLU 5.1 0.2 - - - +
106B THR* 3.4 29.8 - - + +
107B VAL* 6.1 1.4 - - - +
110B CYS* 4.4 7.4 - - - -
112B HIS* 3.2 24.6 + - - +
142B ALA* 3.2 15.9 + - + +
143B PHE* 3.9 4.9 - - - +
144B GLN 3.2 0.2 - - - -
145B ARG* 1.3 82.0 - - - +
147B ALA* 1.3 62.4 + - - +
149B GLN* 3.4 22.0 + - - +
150B CYS* 3.3 23.7 + - - -
307B ILE* 4.2 15.3 - - + -
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Residues in contact with ALA 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B PHE 3.3 9.1 + - - +
144B GLN 3.3 7.8 + - - +
145B ARG 3.2 0.2 - - - -
146B GLU* 1.3 78.5 - - - +
148B ILE* 1.3 62.7 + - - +
149B GLN 3.2 0.2 - - - -
150B CYS* 3.2 26.3 + - - +
151B VAL* 3.2 12.9 + - - +
157B VAL* 4.3 8.7 - - + +
159B VAL* 4.0 18.2 - - + -
170B CYS* 3.8 23.3 - - + -
307B ILE* 4.3 6.2 - - + +
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Residues in contact with ILE 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ARG* 4.1 7.0 - - - +
136B TYR* 4.0 21.5 - - + +
140B LEU* 3.6 30.5 - - + -
144B GLN 3.0 17.4 + - - +
145B ARG* 3.7 7.4 - - + +
147B ALA* 1.3 73.8 - - - +
149B GLN* 1.3 61.3 + - - +
151B VAL* 3.2 9.8 + - - +
152B ASP* 3.0 37.2 + - - +
169B VAL* 4.4 7.0 - - + -
170B CYS* 4.8 10.3 - - - +
173B TYR* 3.9 34.8 - - + -
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Residues in contact with GLN 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B HIS* 5.3 0.3 - - - -
125B LEU* 3.9 26.2 + - + +
126B LYS 4.1 27.8 + - - +
127B PRO* 4.3 10.6 - - + +
128B ARG* 5.6 2.2 - - + +
145B ARG 3.3 10.3 + - - +
146B GLU* 3.6 27.0 - - - +
147B ALA 3.2 0.4 - - - -
148B ILE* 1.3 77.5 - - - +
150B CYS* 1.3 63.2 + - - +
152B ASP* 3.6 12.3 - - + +
153B ASN* 3.3 21.3 + - - +
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Residues in contact with CYS 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B HIS* 4.3 2.5 - - - -
125B LEU* 3.8 16.4 - - - +
146B GLU 3.3 17.0 + - - -
147B ALA* 3.2 9.3 + - - +
149B GLN* 1.3 78.8 - - - +
151B VAL* 1.3 61.6 + - - +
153B ASN* 3.3 8.9 + - - +
154B ASN 3.3 0.2 + - - -
155B GLN* 3.2 24.6 + - - +
157B VAL* 3.7 22.0 - - + -
305B HIS* 3.5 44.2 - - + -
307B ILE* 4.1 8.3 - - - -
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Residues in contact with VAL 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B ALA 3.5 14.4 - - - +
148B ILE* 3.2 9.5 + - - +
150B CYS* 1.3 78.3 - - - +
152B ASP* 1.3 60.2 + - - +
154B ASN* 3.3 17.0 + - - +
155B GLN 4.3 0.7 - - - +
157B VAL* 4.6 6.1 - - + -
170B CYS* 4.5 9.2 - - + +
173B TYR* 4.3 11.0 - - + -
174B ALA* 3.7 31.6 - - + -
177B LEU* 4.4 12.2 - - + +
248B TRP* 3.7 22.7 - - + -
280B VAL* 4.2 22.9 - - + -
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Residues in contact with ASP 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B LYS 5.6 1.3 - - - +
128B ARG* 3.0 47.9 + - + +
148B ILE* 3.0 19.0 + - - +
149B GLN* 3.6 14.6 - - + +
150B CYS 3.3 0.2 - - - -
151B VAL* 1.3 75.9 - - - +
153B ASN* 1.3 60.9 + - - +
154B ASN* 3.2 5.2 + - - +
173B TYR* 2.5 26.5 + - - -
177B LEU* 4.6 13.8 - - - +
180B ARG* 5.2 2.6 + - - -
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Residues in contact with ASN 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU* 2.6 28.3 - - + +
126B LYS* 2.6 56.1 + - - +
149B GLN 3.3 11.5 + - - +
150B CYS 3.7 4.7 - - - +
151B VAL 3.2 0.4 - - - -
152B ASP* 1.3 78.5 + - - +
154B ASN* 1.3 67.6 + - - +
155B GLN* 3.4 11.9 - - + +
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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