Contacts of the helix formed by residues 157 - 164 (chain A) in PDB entry 3GYQ
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 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A ILE* 5.0 3.9 - - - +
152A ILE* 4.3 15.5 - - + +
153A THR* 5.0 7.5 + - - +
154A SER* 3.0 21.4 + - - +
155A ILE 3.2 0.2 - - - -
156A ALA* 1.3 78.8 - - - +
158A ARG* 1.3 64.6 + - - +
159A ARG* 3.0 37.6 + - - +
160A LEU* 2.9 31.9 + - + +
161A GLN 3.1 8.7 + - - -
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Residues in contact with ARG 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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22A THR 5.4 0.4 + - - -
23A LYS* 3.0 32.3 + - - +
24A PRO* 4.2 0.6 - - - +
25A SER* 3.1 38.1 - - - +
156A ALA 3.0 2.4 + - - -
157A ASP* 1.3 77.9 + - - +
159A ARG* 1.3 70.0 + - + +
161A GLN* 3.5 21.3 + - - +
162A ARG* 3.1 61.3 + - - +
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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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127A VAL* 3.7 39.1 - - + +
152A ILE* 5.2 3.8 - - - +
157A ASP* 2.9 24.9 + - - +
158A ARG* 1.3 89.5 - - + +
160A LEU* 1.3 60.0 + - - +
161A GLN 3.3 0.4 - - - -
162A ARG* 4.0 5.9 - - - +
163A ALA* 3.1 28.1 + - - +
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Residues in contact with LEU 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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127A VAL* 4.7 13.0 - - + +
130A ILE* 3.6 33.7 - - + -
131A GLY* 4.3 4.7 - - - +
134A VAL* 5.3 0.9 - - + -
147A LEU* 4.7 6.3 - - + -
152A ILE* 4.1 27.6 - - + -
155A ILE* 4.0 32.1 - - + +
157A ASP* 2.9 17.3 + - + +
159A ARG* 1.3 77.0 - - - +
161A GLN* 1.3 64.7 + - - +
163A ALA* 3.9 0.4 - - - -
164A SER* 2.8 40.5 + - - +
168A VAL* 4.1 16.3 - - + +
173A VAL* 5.4 1.3 - - + -
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Residues in contact with GLN 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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23A LYS* 5.8 3.0 - - - +
32A THR* 3.3 30.4 + - - -
33A LEU 5.0 5.0 + - - -
34A ILE* 6.4 1.1 - - - -
102A VAL* 4.7 0.3 - - - +
155A ILE 4.2 0.4 - - - +
156A ALA* 2.7 33.2 - - - +
157A ASP 3.1 1.9 + - - +
158A ARG* 3.5 22.2 + - - +
160A LEU* 1.3 77.2 - - - +
162A ARG* 1.3 57.4 + - - +
164A SER 2.9 2.8 + - - -
165A ARG 2.9 24.1 + - - -
166A GLY* 3.0 15.9 + - - +
168A VAL* 4.2 24.5 - - + -
169A PHE* 3.8 17.7 - - + -
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Residues in contact with ARG 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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23A LYS* 4.9 14.6 - - - +
89A LYS* 5.3 7.7 - - - +
158A ARG* 3.1 55.9 + - - +
159A ARG* 3.8 6.0 + - - +
161A GLN* 1.3 79.8 - - - +
163A ALA* 1.3 60.3 + - - +
165A ARG* 3.3 16.1 + - - +
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Residues in contact with ALA 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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127A VAL* 3.6 31.2 - - + +
128A GLY* 4.6 6.2 - - - +
131A GLY* 3.4 16.1 - - - -
132A ALA* 3.9 2.4 + - - -
135A ARG* 5.3 2.4 - - - -
159A ARG 3.1 20.9 + - - +
160A LEU* 4.1 5.6 - - - +
162A ARG* 1.3 76.9 - - - +
164A SER* 1.3 58.7 + - - +
165A ARG* 3.3 4.0 + - - +
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Residues in contact with SER 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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131A GLY* 3.3 26.0 + - - -
134A VAL* 3.8 15.5 - - - +
135A ARG* 4.1 3.5 - - - +
160A LEU* 2.8 24.5 + - - +
161A GLN 2.9 4.5 + - - -
163A ALA* 1.3 75.6 - - - +
165A ARG* 1.3 61.8 + - - +
166A GLY 2.8 13.5 + - - -
167A TYR* 2.9 20.1 + - - +
168A VAL* 3.9 24.8 - - - +
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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