Contacts of the helix formed by residues 153 - 162 (chain A) in PDB entry 3IH9
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 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A VAL* 5.5 0.2 - - - +
61A THR* 3.9 5.4 - - + -
151A SER 3.8 2.0 + - - -
152A VAL* 1.3 70.5 - - - +
154A TRP* 1.3 59.1 + - - +
155A GLU* 3.1 12.9 + - - +
156A THR* 2.6 43.1 + - - -
157A TYR 3.1 14.7 + - - -
196A ALA* 2.8 22.7 + - - +
198A LEU* 3.5 34.2 - - + +
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Residues in contact with TRP 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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135A LEU* 4.1 22.9 - - + -
152A VAL* 3.0 50.5 + - + +
153A ASP* 1.3 68.3 - - - +
155A GLU* 1.3 60.4 + - - +
157A TYR* 3.4 41.7 - + + +
158A GLU* 2.9 38.4 + - + +
193A ALA* 4.4 6.5 - - + -
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Residues in contact with GLU 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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30A VAL* 3.8 23.4 - - + +
153A ASP* 3.1 12.4 + - - +
154A TRP* 1.3 79.2 - - - +
156A THR* 1.3 63.4 + - - +
158A GLU* 3.9 5.1 - - - +
159A SER* 3.2 22.5 + - - -
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Residues in contact with THR 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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27A TYR* 5.4 0.2 - - - +
28A ILE* 4.0 20.8 - - + +
30A VAL* 3.9 18.6 - - + +
31A LEU* 5.1 5.3 - - + +
61A THR* 3.9 18.5 + - + +
63A GLN* 4.0 21.5 - - - +
153A ASP* 2.6 28.6 + - - -
155A GLU* 1.3 70.0 - - - +
157A TYR* 1.3 61.5 - - - +
159A SER* 3.2 7.3 + - - -
160A GLU* 2.8 30.4 + - + +
196A ALA* 4.7 4.0 - - + -
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Residues in contact with TYR 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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131A ARG* 5.1 3.1 + - - -
152A VAL* 4.7 0.2 - - + -
153A ASP 3.1 13.0 + - - +
154A TRP* 3.4 37.2 - + + +
156A THR* 1.3 76.5 - - - +
158A GLU* 1.3 84.9 + - - +
160A GLU* 3.1 4.4 + - - +
161A MET* 2.9 57.3 + - + +
189A ALA* 3.5 40.2 - - - +
192A VAL* 3.4 22.0 - - + -
193A ALA* 3.8 15.3 - - + -
196A ALA* 4.3 10.5 - - + +
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Residues in contact with GLU 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 TRP* 2.9 25.7 + - + +
155A GLU* 3.9 5.6 - - - +
157A TYR* 1.3 103.7 - - - +
159A SER* 1.3 64.2 + - - +
160A GLU 3.2 0.7 + - - -
161A MET* 3.2 9.0 + - - +
162A ALA* 3.2 21.8 + - - +
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Residues in contact with SER 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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28A ILE* 3.1 36.1 - - - +
29A PRO* 3.9 13.0 - - - +
30A VAL* 3.7 17.0 - - - +
155A GLU* 3.2 12.7 + - - -
156A THR 3.2 8.5 + - - -
158A GLU* 1.3 79.8 - - - +
160A GLU* 1.3 61.2 + - - +
162A ALA* 3.6 12.2 + - - +
163A VAL* 3.7 7.1 - - - +
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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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27A TYR* 2.7 38.5 + - + +
28A ILE* 3.9 8.2 - - + +
63A GLN* 4.0 12.5 + - - +
156A THR* 2.8 16.1 + - + +
157A TYR 3.4 7.2 - - - +
159A SER* 1.3 73.8 - - - +
161A MET* 1.3 58.5 + - - +
162A ALA 3.1 1.8 - - - -
163A VAL* 3.0 22.7 + - - +
164A SER* 2.6 21.6 + - - +
167A ASN* 4.3 13.6 + - - -
192A VAL* 3.2 37.7 - - + +
195A CYS* 5.4 2.4 - - - +
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Residues in contact with MET 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 TYR* 2.9 56.9 + - + +
158A GLU* 3.2 10.0 + - - +
160A GLU* 1.3 72.7 - - - +
162A ALA* 1.3 60.7 + - - +
163A VAL 3.2 1.0 + - - -
164A SER* 3.2 23.7 + - - -
168A LEU* 5.8 2.2 - - + +
185A GLU* 4.7 15.9 - - + +
188A VAL* 4.7 2.9 - - + -
189A ALA* 3.6 36.6 - - + +
192A VAL* 4.1 11.2 - - + -
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Residues in contact with ALA 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 GLU 3.2 11.5 + - - +
159A SER* 3.7 12.8 - - - +
160A GLU 3.1 0.8 - - - -
161A MET* 1.3 77.9 - - - +
163A VAL* 1.3 66.7 + - + +
164A SER 3.8 0.4 - - - -
165A ASP* 5.3 1.7 - - - +
175B ARG* 6.0 0.2 + - - -
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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