Contacts of the helix formed by residues 158 - 165 (chain A) in PDB entry 1A1A
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 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A THR* 1.3 71.3 - - - +
159A ARG* 1.3 64.8 + - - +
161A SER* 2.7 22.3 + - - -
162A GLU* 3.1 24.7 + - - +
178A ARG* 3.3 23.3 - - - +
181A GLU* 2.8 19.2 + - - +
204A HIS* 3.5 29.6 + - + +
153B PHE* 4.0 34.8 + - + +
156B ILE* 3.5 25.8 - - - +
164B LEU* 4.9 4.0 - - + -
100C ACE 3.0 35.2 + - - +
101C PTH 2.6 39.9 + - - +
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Residues in contact with ARG 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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157A THR* 3.2 1.0 - - - -
158A ARG* 1.3 83.8 - - - +
160A GLU* 1.4 56.8 + - - +
162A GLU* 3.3 10.8 + - - +
163A ARG* 2.9 27.0 + - + +
150B GLU* 2.7 62.6 + - + +
153B PHE* 3.8 17.7 - - + -
247B VAL* 3.4 24.5 + - - +
248B CYS 2.8 27.1 + - - -
249B PRO* 3.2 24.4 + - - +
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Residues in contact with GLU 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 ILE* 4.0 24.0 - - + -
157A THR* 2.9 26.3 + - - +
159A ARG* 1.4 74.4 - - - +
161A SER* 1.4 64.7 + - - +
163A ARG* 2.6 53.9 + - - +
164A LEU* 2.9 33.1 + - + +
249B PRO* 4.3 1.5 + - - +
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Residues in contact with SER 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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156A ILE* 3.7 19.4 - - - +
157A THR 2.9 11.9 + - - -
158A ARG* 2.7 20.3 + - - -
160A GLU* 1.4 75.6 - - - +
162A GLU* 1.3 55.9 + - - +
164A LEU* 3.3 2.1 + - - +
165A LEU* 2.8 36.9 + - - +
176A LEU* 3.9 24.0 - - - -
178A ARG* 3.3 19.8 + - - -
190A SER* 3.7 8.5 + - - -
204A HIS* 3.8 4.7 - - - -
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Residues in contact with GLU 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 ARG* 3.1 23.3 + - - +
159A ARG* 3.5 11.1 - - - +
161A SER* 1.3 72.4 + - - +
163A ARG* 1.3 59.5 + - - +
166A LEU* 2.7 54.7 + - + +
202A VAL* 3.6 32.5 - - + -
204A HIS* 2.7 30.9 + - + +
152B TYR 4.9 8.3 - - - +
153B PHE* 6.2 0.3 - - - -
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Residues in contact with ARG 163 (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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159A ARG* 2.9 14.6 + - + +
160A GLU* 2.6 50.9 + - - +
162A GLU* 1.3 78.1 - - - +
164A LEU* 1.3 80.2 + - - +
166A LEU* 3.9 6.7 + - - +
167A ASN* 4.0 9.4 + - - +
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Residues in contact with LEU 164 (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 PHE* 3.7 31.4 - - + -
156A ILE* 3.8 22.9 - - + -
160A GLU* 2.9 21.2 + - + +
161A SER* 3.8 4.0 - - - +
163A ARG* 1.3 105.1 - - - +
165A LEU* 1.3 60.5 + - - +
167A ASN* 3.6 8.9 - - - +
170A ASN* 2.9 18.0 + - - -
176A LEU* 4.5 1.8 - - + -
248A CYS* 3.7 17.8 - - - -
249A PRO 5.0 7.0 - - - +
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Residues in contact with LEU 165 (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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161A SER 2.8 25.2 + - - +
164A LEU* 1.3 71.2 - - - +
166A LEU* 1.3 56.6 + - - +
167A ASN 3.1 11.0 + - - +
170A ASN* 3.1 13.2 + - - +
174A THR* 3.7 27.8 - - + +
175A PHE* 3.9 8.3 - - - -
176A LEU* 3.9 12.3 - - + -
190A SER* 3.5 41.3 - - - +
191A VAL* 4.2 1.1 - - - +
192A SER* 3.8 17.6 - - - -
202A VAL* 3.8 23.1 - - + -
248A CYS* 3.7 27.4 - - + -
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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