Contacts of the helix formed by residues 138 - 149 (chain I) in PDB entry 6AHU
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 LYS 138 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110I GLU* 5.4 14.6 - - + +
113I PHE* 5.5 2.8 - - - -
114I HIS* 5.7 3.5 - - + -
136I TYR 4.1 1.7 + - - +
137I PHE* 1.3 73.2 - - - +
139I ARG* 1.3 68.0 + - - +
140I PRO* 3.7 25.4 - - + +
141I PRO* 3.3 26.4 - - + +
142I ILE* 3.3 20.6 - - - +
179I ILE* 4.6 1.3 - - - -
232L GLU* 4.7 15.5 + - - +
268L GLU* 3.3 37.3 + - + +
269L PRO* 6.4 0.2 - - - -
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Residues in contact with ARG 139 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138I LYS* 1.3 72.4 - - - +
140I PRO* 1.3 73.9 - - + +
142I ILE* 3.3 3.5 + - - +
143I ASN* 2.9 39.4 + - - +
178I GLN 5.9 0.2 + - - -
179I ILE* 3.8 39.6 + - + +
236L ARG* 3.1 43.2 - - - +
238L LEU* 6.2 0.6 - - - +
239L GLU* 3.2 30.3 + - - +
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Residues in contact with PRO 140 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138I LYS* 3.7 25.4 - - + -
139I ARG* 1.3 93.9 - - + +
141I PRO* 1.4 67.1 - - + +
143I ASN* 3.5 8.7 + - + +
144I VAL* 3.3 29.4 + - + +
231L PRO* 4.5 17.9 - - + -
232L GLU* 3.8 34.1 - - + +
268L GLU 6.0 2.2 - - - +
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Residues in contact with PRO 141 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110I GLU 6.0 1.3 - - - +
113I PHE* 4.0 26.2 - - + -
114I HIS* 4.3 31.4 - - + -
117I CYS* 3.4 28.5 - - + +
118I THR* 5.8 1.8 - - - +
138I LYS* 3.3 36.8 - - + +
140I PRO* 1.4 97.4 - - + +
142I ILE* 1.3 59.1 + - - -
144I VAL* 4.0 4.3 + - + +
145I ALA* 3.7 7.3 + - - +
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Residues in contact with ILE 142 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113I PHE* 3.7 23.6 - - + -
137I PHE* 4.7 4.7 - - + -
138I LYS 3.3 18.8 - - - +
139I ARG 3.3 7.1 + - - +
140I PRO 3.2 0.6 - - - -
141I PRO* 1.3 75.4 - - - +
143I ASN* 1.3 67.6 + - - +
144I VAL 3.2 0.4 - - - -
145I ALA* 3.2 11.3 + - - +
146I ILE* 3.2 17.9 + - + +
152I PHE* 3.7 26.9 - - + -
176I LEU* 4.3 16.4 - - + -
179I ILE* 3.8 18.8 - - + +
180I CYS* 3.8 38.1 - - + -
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Residues in contact with ASN 143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139I ARG* 2.9 39.2 + - - +
140I PRO* 3.5 8.4 + - + +
141I PRO 3.5 0.2 - - - -
142I ILE* 1.3 78.1 - - - +
144I VAL* 1.3 61.9 + - + +
146I ILE* 3.4 28.7 - - + +
147I ASP* 3.9 6.9 + - - +
179I ILE* 4.9 8.2 - - - +
183I LYS* 5.5 1.9 + - - -
231L PRO* 6.2 3.6 - - + +
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Residues in contact with VAL 144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114I HIS* 6.4 0.2 - - - +
117I CYS 4.1 9.6 - - - +
118I THR* 3.9 27.8 - - + +
140I PRO* 3.3 19.2 + - + +
141I PRO* 4.4 5.8 - - + +
142I ILE 3.2 0.6 - - - -
143I ASN* 1.3 78.3 - - + +
145I ALA* 1.3 59.1 + - - +
146I ILE 3.3 0.4 - - - -
147I ASP* 3.3 5.4 + - - +
148I ARG* 2.9 29.8 + - + +
231L PRO* 6.5 0.7 - - + -
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Residues in contact with ALA 145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117I CYS* 4.1 8.5 + - + -
141I PRO 3.7 12.4 + - - +
142I ILE 3.2 2.9 + - - +
144I VAL* 1.3 79.5 - - - +
146I ILE* 1.3 57.9 + - - +
148I ARG* 3.5 4.0 + - - -
149I GLY 3.1 5.7 + - - -
150I LEU* 2.8 57.7 + - + +
152I PHE* 3.7 29.4 - - + -
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Residues in contact with ILE 146 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142I ILE* 3.2 21.4 + - + +
143I ASN* 3.4 27.6 - - + +
145I ALA* 1.3 76.5 - - - +
147I ASP* 1.3 74.1 + - + +
149I GLY* 3.7 8.1 + - - -
152I PHE* 4.8 3.4 - - + -
180I CYS* 4.3 18.6 - - - +
183I LYS* 3.4 53.1 - - + +
184I ASN* 3.4 28.3 + - - +
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Residues in contact with ASP 147 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143I ASN 4.0 10.1 - - - +
144I VAL* 3.3 9.4 + - + +
146I ILE* 1.3 84.3 - - + +
148I ARG* 1.3 65.6 + - - +
149I GLY* 4.7 0.2 - - - -
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Residues in contact with ARG 148 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116I ALA 4.1 1.8 + - - -
117I CYS 3.3 22.9 + - - -
118I THR* 3.0 28.0 + - - +
120I LEU 3.2 22.5 + - - -
121I ASP* 2.6 35.2 + - - +
122I VAL 4.5 7.2 + - - +
144I VAL* 2.9 20.2 + - + +
145I ALA* 3.9 5.8 - - - +
147I ASP* 1.3 80.3 + - - +
149I GLY* 1.3 55.9 + - - +
150I LEU* 4.4 14.5 - - - +
231I HIS* 3.9 22.1 + - + +
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Residues in contact with GLY 149 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123I ASP 4.7 2.8 - - - +
145I ALA 3.1 3.9 + - - -
146I ILE 3.7 4.6 + - - -
147I ASP 3.3 3.4 + - - -
148I ARG* 1.3 79.6 - - - +
150I LEU* 1.3 62.3 + - - +
151I ALA* 3.7 3.3 + - - +
184I ASN* 3.5 12.5 + - - -
227I ALA* 5.7 1.0 - - - +
231I HIS* 4.7 21.8 + - - +
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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