Contacts of the helix formed by residues 153 - 162 (chain A) in PDB entry 1A76
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 GLY 153 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ASP* 5.0 6.1 - - - -
78A VAL* 3.5 14.9 - - - +
79A PHE 3.9 17.9 - - - -
80A ASP* 2.7 23.6 + - - -
149A ALA* 3.9 4.7 - - - -
151A SER 3.3 1.2 + - - -
152A GLU* 1.3 70.5 - - - +
154A GLU* 1.3 60.8 + - - +
156A GLN 3.2 0.7 + - - -
157A ALA* 2.9 30.3 + - - +
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Residues in contact with GLU 154 (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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27A ASP* 3.6 21.7 + - - +
152A GLU* 2.8 34.0 - - + +
153A GLY* 1.3 80.1 + - - +
155A ALA* 1.3 55.0 + - - +
157A ALA* 3.6 6.0 + - - +
158A SER* 2.6 36.8 + - - -
169A VAL* 5.7 1.8 - - + -
175A ASP* 5.3 6.1 - - + +
176A ALA* 4.7 12.3 - - + +
179A TYR* 3.6 26.7 + - + -
224A ASP* 4.5 0.5 - - - +
340A MN 2.2 34.2 + - - -
341A MN 3.8 15.2 + - - -
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Residues in contact with ALA 155 (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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88A GLU* 4.7 0.9 - - + +
152A GLU* 3.2 17.6 + - + +
153A GLY 3.1 0.4 - - - -
154A GLU* 1.3 79.8 - - - +
156A GLN* 1.3 66.2 + - - +
158A SER* 3.4 2.6 + - - -
159A TYR* 3.1 22.5 + - - +
179A TYR* 3.5 38.8 - - + +
268A PRO* 3.8 22.5 - - + +
269A LYS 5.1 4.3 - - - +
270A VAL* 5.1 1.1 - - - +
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Residues in contact with GLN 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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78A VAL* 3.6 15.9 - - + -
147A VAL* 4.4 4.9 - - + +
149A ALA* 3.3 28.0 - - + -
150A PRO* 3.6 3.3 - - + +
152A GLU 3.2 3.4 + - - -
153A GLY 3.6 4.7 - - - +
155A ALA* 1.3 79.9 - - - +
157A ALA* 1.3 61.3 + - - +
159A TYR* 3.3 3.8 + - - +
160A MET* 3.1 49.0 + - - +
269A LYS 5.4 0.8 + - - +
270A VAL* 2.8 35.7 - - - +
271A THR* 2.9 45.7 + - - +
274A TYR* 3.7 5.5 - - - -
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Residues in contact with ALA 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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25A ALA* 3.8 23.6 - - + +
27A ASP* 5.1 4.3 - - - +
78A VAL* 4.1 10.1 - - + +
153A GLY 2.9 17.4 + - - +
154A GLU* 3.9 5.4 - - - +
156A GLN* 1.3 74.1 - - - +
158A SER* 1.3 66.3 + - - +
160A MET* 3.3 8.3 + - - +
161A ALA* 3.1 17.7 + - - +
169A VAL* 3.3 32.2 - - + +
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Residues in contact with SER 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 GLU 2.6 23.8 + - - -
155A ALA 3.7 2.5 - - - -
156A GLN 3.3 0.2 - - - -
157A ALA* 1.3 76.8 - - - +
159A TYR* 1.3 52.0 + - - +
161A ALA* 3.0 4.3 + - - +
162A LYS* 2.7 39.1 + - - +
169A VAL* 3.7 8.2 - - - +
176A ALA* 3.3 25.5 + - - +
179A TYR* 3.5 26.2 - - - +
181A ALA* 3.8 15.3 - - - -
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Residues in contact with TYR 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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155A ALA 3.1 12.1 + - - +
156A GLN* 3.5 10.5 - - - +
157A ALA 3.3 0.2 - - - -
158A SER* 1.3 78.4 - - - +
160A MET* 1.3 58.7 + - + +
162A LYS* 3.3 23.0 + - + +
163A LYS* 2.9 64.0 + - + +
268A PRO* 6.2 1.8 - - + -
270A VAL* 2.6 48.9 - - + +
271A THR 3.6 9.4 - - - -
272A ASP* 2.6 36.8 + - - -
274A TYR* 4.9 0.4 - - - -
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Residues in contact with MET 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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25A ALA* 4.5 1.6 - - + -
76A ILE* 3.8 35.9 - - + -
78A VAL* 4.0 14.1 - - + -
147A VAL* 3.9 18.8 - - + -
156A GLN* 3.1 46.8 + - - +
157A ALA* 3.6 7.0 - - - +
159A TYR* 1.3 77.8 - - + +
161A ALA* 1.3 60.2 + - - +
163A LYS* 3.6 2.8 + - - +
164A GLY 3.3 2.9 + - - -
165A ASP* 3.0 30.8 + - + +
166A VAL* 3.5 13.7 + - + -
274A TYR* 3.7 34.5 - - + +
276A LEU* 5.4 1.1 - - + -
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Residues in contact with ALA 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 ALA 3.1 12.5 + - - +
158A SER 3.0 8.2 + - - +
160A MET* 1.3 76.7 - - - +
162A LYS* 1.3 66.3 + - - +
164A GLY* 3.0 12.0 + - - -
166A VAL* 3.4 30.2 - - + +
167A TRP 4.8 1.5 - - - +
168A ALA* 4.4 10.3 - - - -
169A VAL* 4.1 13.9 - - + +
181A ALA* 5.0 0.2 - - + -
182A PRO* 3.8 24.0 - - + +
183A ARG* 5.0 1.1 + - - +
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Residues in contact with LYS 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 SER 2.7 20.2 + - - +
159A TYR* 3.6 21.1 - - + +
161A ALA* 1.3 74.8 - - - +
163A LYS* 1.3 61.2 + - + +
164A GLY* 3.2 1.6 + - - -
179A TYR 3.4 16.1 + - - +
180A GLY* 2.9 40.8 - - - +
182A PRO* 3.7 12.6 - - + +
268A PRO* 6.2 2.2 - - - +
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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