Contacts of the helix formed by residues 155 - 162 (chain A) in PDB entry 2W2Q
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 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A ILE* 1.3 89.8 - - + +
156A TRP* 1.3 67.0 + - - +
157A ASN* 3.0 23.2 + - - +
158A LEU* 3.1 33.4 + - + -
159A GLU* 3.3 9.0 + - - +
238A ASP 5.3 0.7 - - - +
239A ALA* 4.7 3.8 - - + +
369A ILE* 4.3 27.6 - - + +
298E LEU* 3.4 39.9 - - + +
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Residues in contact with TRP 156 (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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154A ILE 3.4 4.2 + - - -
155A PRO* 1.3 70.8 - - - +
157A ASN* 1.3 64.2 + - + +
159A GLU* 3.4 12.1 - - - +
160A ARG* 3.0 58.3 + - + +
339A THR* 3.8 4.5 - - - -
340A ASN* 3.3 22.2 - - - -
341A ALA* 3.6 39.6 - - + +
364A PRO* 3.5 31.4 - - + -
366A GLU 3.0 29.7 + - - -
367A ASP* 3.2 24.2 + - + +
368A ILE* 4.1 1.6 - - + -
369A ILE* 6.6 0.2 - - + -
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Residues in contact with ASN 157 (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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155A PRO* 3.2 20.8 - - - +
156A TRP* 1.3 96.1 + - + +
158A LEU* 1.3 79.9 + - - +
160A ARG* 3.5 1.9 + - - +
161A ILE* 3.4 28.2 + - - +
233A VAL* 5.4 0.6 - - - +
239A ALA 5.1 1.6 + - - -
364A PRO* 3.5 18.1 - - + +
367A ASP 4.4 0.5 - - - +
368A ILE* 3.6 31.4 - - + +
369A ILE 4.4 2.9 + - - -
391A HIS* 2.8 35.3 + - - +
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Residues in contact with LEU 158 (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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154A ILE* 3.6 16.4 - - + -
155A PRO* 3.1 23.2 + - + +
157A ASN* 1.3 90.5 - - - +
159A GLU* 1.3 61.2 + - - +
161A ILE* 3.3 13.6 - - + +
162A THR* 2.8 26.9 + - - -
233A VAL* 5.2 0.9 - - + +
238A ASP 4.5 1.6 - - - +
239A ALA* 3.4 39.0 - - - +
240A GLY 3.8 12.1 - - - +
241A VAL* 3.7 30.5 - - + -
243A LYS* 4.1 9.6 - - - +
391A HIS* 4.6 0.2 - - - +
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Residues in contact with GLU 159 (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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153A SER* 5.4 1.6 + - - -
154A ILE* 3.5 38.4 + - + +
155A PRO 3.3 6.5 + - - +
156A TRP* 3.4 14.5 - - - +
158A LEU* 1.3 79.8 - - - +
160A ARG* 1.3 61.4 + - - +
162A THR* 3.1 26.4 + - - +
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Residues in contact with ARG 160 (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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156A TRP* 3.0 46.2 + - + +
157A ASN 3.7 6.7 - - - +
158A LEU 3.3 0.8 - - - -
159A GLU* 1.3 78.3 - - - +
161A ILE* 1.3 58.4 + - - +
162A THR 3.7 2.3 + - - +
340A ASN 4.1 1.2 + - - -
341A ALA* 2.8 38.5 + - - +
343A ASP* 3.2 41.8 + - - +
364A PRO* 4.4 8.5 - - + -
441A VAL* 5.0 8.4 - - + +
442A ALA 4.7 3.3 - - - +
443A ALA* 4.8 3.8 - - - +
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Residues in contact with ILE 161 (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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157A ASN 3.4 14.3 + - - +
158A LEU* 3.3 20.2 - - + +
160A ARG* 1.3 75.8 - - + +
162A THR* 1.3 60.3 + - - +
163A PRO* 3.3 4.7 - - - +
241A VAL* 3.6 42.0 - - + -
364A PRO* 3.9 22.7 - - + -
391A HIS* 4.3 7.0 - - + -
395A ILE* 4.3 15.9 - - + -
442A ALA 3.5 23.8 - - - +
443A ALA* 3.4 6.8 - - - +
444A LEU* 2.7 44.6 + - + +
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Residues in contact with THR 162 (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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158A LEU 2.8 21.1 + - - -
159A GLU* 3.1 17.7 + - - +
160A ARG 4.6 2.8 - - - +
161A ILE* 1.3 79.4 - - - +
163A PRO* 1.4 77.3 - - + +
164A PRO* 3.8 2.9 - - - +
444A LEU* 4.4 11.7 - - + +
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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