Contacts of the helix formed by residues 294 - 305 (chain A) in PDB entry 1IAX
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 ASN 294 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ARG* 3.7 1.3 - - - -
233A HIS* 5.1 0.4 + - - -
267A LYS 3.7 2.2 + - - -
268A ASP* 2.9 50.3 + - - +
271A HIS* 4.1 0.2 - - + -
292A SER* 3.1 12.1 - - - +
293A PHE* 1.3 78.1 - - - +
295A ASP* 1.3 58.3 + - - +
296A ASP* 2.7 37.8 + - - +
297A VAL* 2.9 23.2 + - + +
298A VAL* 2.9 29.6 + - - +
12B LEU* 4.2 13.5 - - - +
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Residues in contact with ASP 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ARG* 2.7 30.3 + - - +
268A ASP* 5.3 3.1 + - - +
293A PHE 4.1 3.8 - - - +
294A ASN* 1.3 73.8 + - - +
296A ASP* 1.3 60.1 + - - +
298A VAL* 3.4 5.7 - - - +
299A ASN* 2.9 37.5 + - - +
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Residues in contact with ASP 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ASN* 2.7 15.3 + - - +
295A ASP* 1.3 72.8 - - - +
297A VAL* 1.3 65.2 + - - +
299A ASN* 2.9 14.2 + - - +
300A CYS* 2.9 24.2 + - - +
12B LEU* 3.6 19.8 - - + +
16B ALA* 5.5 5.3 - - - +
19B GLU 5.1 6.4 - - - +
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Residues in contact with VAL 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ILE* 3.9 23.1 - - + -
137A CYS* 4.3 12.1 - - + -
138A LEU* 4.1 3.6 - - + -
271A HIS* 3.8 9.4 - - + -
290A ILE* 5.1 0.4 - - + -
292A SER* 3.2 30.3 - - - +
294A ASN* 2.9 22.8 + - + +
296A ASP* 1.3 75.0 - - - +
298A VAL* 1.3 54.5 + - - +
300A CYS* 3.3 5.9 + - - +
301A ALA* 2.8 37.5 + - + +
12B LEU* 3.4 34.1 - - + +
16B ALA* 5.5 0.2 - - - -
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Residues in contact with VAL 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLU 4.7 0.2 - - - +
120A ARG* 3.0 41.7 - - + +
122A VAL* 4.0 12.5 - - + +
290A ILE* 6.2 0.7 - - - -
292A SER* 3.4 18.2 - - - +
294A ASN 2.9 26.8 + - - +
295A ASP* 3.4 9.0 - - - +
296A ASP 3.1 0.2 - - - -
297A VAL* 1.3 77.9 - - - +
299A ASN* 1.3 63.2 + - - +
301A ALA* 3.8 5.2 - - - +
302A ARG* 3.0 52.3 + - - +
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Residues in contact with ASN 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ASP* 2.9 29.0 + - - +
296A ASP* 2.9 15.6 + - - +
298A VAL* 1.3 76.0 - - - +
300A CYS* 1.3 62.1 + - - +
302A ARG* 3.1 26.1 + - - +
303A LYS* 3.1 33.0 + - - +
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Residues in contact with CYS 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A CYS* 3.3 23.6 - - - -
296A ASP 2.9 16.4 + - - +
297A VAL 3.8 1.3 - - - +
299A ASN* 1.3 70.7 - - - +
301A ALA* 1.3 65.2 + - - +
303A LYS* 3.1 6.7 + - - +
304A MET* 2.9 31.9 + - - +
16B ALA* 3.3 41.5 - - + +
19B GLU* 3.6 20.4 - - - +
161B TRP* 3.8 13.7 - - - -
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Residues in contact with ALA 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A VAL* 3.6 21.0 - - + +
123A MET 4.7 0.9 - - - +
133A THR* 4.3 8.0 - - - +
137A CYS* 3.8 12.9 - - - -
290A ILE* 4.2 30.2 - - + +
297A VAL* 2.8 24.2 + - + +
298A VAL* 3.8 5.6 - - - +
300A CYS* 1.3 72.0 - - - +
302A ARG* 1.3 62.4 + - - +
304A MET* 3.3 3.3 + - - +
305A SER* 3.0 17.5 + - - -
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Residues in contact with ARG 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A TYR* 3.7 26.9 - - + +
93A HIS* 3.4 49.8 + - - +
99A ARG* 4.9 1.2 - - - +
119A GLU 3.1 24.9 + - - -
121A VAL 4.5 5.2 + - - +
122A VAL* 3.8 23.7 - - + +
298A VAL* 3.0 33.4 + - - +
299A ASN* 3.3 26.3 + - - +
300A CYS 3.1 0.2 - - - -
301A ALA* 1.3 74.5 - - - +
303A LYS* 1.3 66.1 + - + +
305A SER* 2.5 24.9 + - - -
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Residues in contact with LYS 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A TYR* 4.3 10.4 - - + -
299A ASN* 3.1 23.8 + - - +
300A CYS 3.1 7.7 + - - +
302A ARG* 1.3 76.8 - - - +
304A MET* 1.3 55.0 + - - +
306A SER* 2.7 28.8 + - - -
307A PHE* 4.9 1.0 - - - -
19B GLU* 3.2 47.8 - - - +
157B ARG* 4.1 13.4 + - - +
161B TRP* 3.8 14.6 - - + -
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Residues in contact with MET 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A THR* 3.4 33.1 + - + +
136A PHE* 3.9 20.2 - - + -
137A CYS* 4.4 4.7 - - - -
300A CYS* 2.9 23.0 + - - +
301A ALA 3.5 8.1 - - - +
302A ARG 3.1 0.2 - - - -
303A LYS* 1.3 74.2 - - - +
305A SER* 1.3 61.1 + - - +
306A SER* 3.0 7.1 + - - -
307A PHE* 3.1 27.5 + - - +
308A GLY 4.2 0.9 + - - -
15B LEU* 4.0 8.5 - - + -
161B TRP* 3.5 30.5 - - + -
162B ARG* 3.1 47.9 + - + +
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Residues in contact with SER 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A TYR* 3.7 12.7 + - - +
122A VAL* 4.2 4.9 - - - +
123A MET 3.4 28.9 - - - -
124A ALA* 5.4 1.8 - - - +
301A ALA 3.0 9.1 + - - -
302A ARG* 2.5 24.3 + - - -
304A MET* 1.3 74.1 - - - +
306A SER* 1.3 63.7 + - - +
307A PHE 3.0 0.4 - - - -
308A GLY 3.1 12.1 + - - +
309A LEU* 2.8 41.6 + - - +
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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