Contacts of the helix formed by residues 144 - 158 (chain A) in PDB entry 3H1I
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 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A GLU 4.1 0.6 + - - +
141A MET* 3.2 16.3 + - - +
142A ASP 3.3 0.6 - - - -
143A ASN* 1.3 76.3 - - - +
145A MET* 1.3 63.0 + - - +
146A THR* 3.3 22.1 + - - -
147A ASN* 2.8 36.5 + - - +
148A VAL* 3.1 11.8 + - - +
47I ARG* 5.1 9.0 - - - +
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Residues in contact with MET 145 (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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142A ASP 4.1 18.4 - - - +
143A ASN* 3.4 15.1 + - - +
144A ASP* 1.3 71.9 + - - +
146A THR* 1.3 65.7 + - - +
147A ASN 3.0 0.5 + - - -
148A VAL* 3.0 12.9 + - + +
149A THR* 2.7 26.8 + - - +
248A LEU* 3.7 33.7 - - + -
249A PRO* 6.1 4.5 - - + -
250A VAL* 5.1 4.7 - - + +
252A HIS* 3.0 40.6 - - + +
425A VAL* 4.3 17.2 - - + +
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Residues in contact with THR 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ASP* 3.1 11.7 + - - -
145A MET* 1.3 77.4 - - - +
147A ASN* 1.3 64.8 + - - +
149A THR* 3.2 3.0 - - - -
150A PHE* 2.9 40.6 + - + -
252A HIS* 3.6 17.7 - - - -
308A GLN* 4.2 8.1 - - - +
323A HIS* 3.5 27.5 - - + +
325A VAL* 5.6 0.2 - - - +
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Residues in contact with ASN 147 (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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141A MET* 4.2 28.7 + - + +
144A ASP* 2.8 40.2 + - + +
146A THR* 1.3 72.2 - - - +
148A VAL* 1.3 66.4 + - - +
149A THR 2.6 6.7 + - - -
150A PHE* 2.6 19.9 + - - +
151A ASP* 3.0 22.9 + - - +
2E HIS* 5.5 1.3 - - + +
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Residues in contact with VAL 148 (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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141A MET 4.1 1.6 - - - +
142A ASP* 3.5 35.2 - - - +
144A ASP 3.1 9.4 + - - +
145A MET* 3.0 13.4 + - + +
147A ASN* 1.3 77.2 - - - +
149A THR* 1.3 60.9 + - - +
151A ASP 3.9 0.4 + - - -
152A TYR* 3.2 48.6 + - + +
425A VAL* 4.3 16.6 - - + -
2E HIS* 3.6 36.4 + - + +
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Residues in contact with THR 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A MET 2.7 15.4 + - - -
146A THR* 3.2 11.9 - - - +
147A ASN 2.6 4.2 + - - -
148A VAL* 1.3 71.2 - - - +
150A PHE* 1.3 54.7 + - + +
152A TYR* 3.2 4.8 + - - +
153A LEU* 2.7 32.4 + - - +
252A HIS* 3.4 21.5 + - - +
253A VAL 4.8 0.7 - - - -
254A ALA* 3.4 34.3 - - + +
323A HIS* 4.0 13.7 - - + -
423A ALA* 3.8 10.1 - - + +
425A VAL* 3.5 18.2 - - - +
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Residues in contact with PHE 150 (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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92A ARG* 6.0 0.2 - - - +
146A THR* 2.9 42.2 - - + -
147A ASN* 2.6 14.2 + - - +
149A THR* 1.3 76.9 - - + +
151A ASP* 1.3 56.6 + - - +
153A LEU* 3.3 14.6 - - + +
154A HIS* 2.7 51.1 + + + +
254A ALA* 5.4 0.7 - - + -
308A GLN* 4.6 9.6 - - - -
310A PHE* 3.8 39.9 - + + -
312A THR* 5.2 3.8 - - - -
319A LEU* 6.4 0.2 - - + -
323A HIS* 4.1 30.3 - + + -
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Residues in contact with ASP 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ARG* 3.1 25.4 + - - +
147A ASN* 3.0 18.8 + - - +
150A PHE* 1.3 76.7 - - - +
152A TYR* 1.3 53.0 + - + +
154A HIS* 3.1 3.8 + - - +
155A ALA* 2.5 38.1 + - - +
164A ALA 5.1 0.7 - - - +
166A THR* 3.8 22.9 - - + +
167A VAL* 5.2 2.8 + - - +
168A GLU* 4.4 8.1 - - - +
2E HIS* 2.4 42.4 + - + +
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Residues in contact with TYR 152 (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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148A VAL* 3.2 35.5 + - + +
149A THR* 3.2 4.7 + - - +
151A ASP* 1.3 77.2 - - - +
153A LEU* 1.3 66.9 + - - +
155A ALA* 3.0 19.1 + - + +
156A THR* 3.0 15.8 + - - -
241A ILE* 3.7 32.3 - - + +
243A ALA* 3.5 26.4 - - + +
423A ALA* 4.8 2.0 - - + -
424A ALA 5.1 0.7 - - - -
425A VAL* 3.9 14.1 - - + -
238D ARG* 4.9 1.9 + - - -
2E HIS* 3.7 31.5 - + + +
5E VAL* 3.8 39.5 - - + +
14G ILE* 4.1 10.9 - - + +
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Residues in contact with LEU 153 (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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149A THR 2.7 17.8 + - - +
150A PHE* 3.3 18.8 - - + +
152A TYR* 1.3 72.4 - - - +
154A HIS* 1.3 53.3 + - + +
156A THR* 3.4 3.7 - - + +
157A ALA* 2.7 39.1 + - + +
254A ALA* 4.4 12.8 - - + +
256A ALA* 4.4 8.5 - - + -
310A PHE* 4.3 24.2 - - + -
319A LEU* 3.7 25.1 - - + -
421A ALA* 3.7 37.5 - - + +
422A LEU 4.6 1.1 - - - +
423A ALA* 3.7 20.8 - - + +
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Residues in contact with HIS 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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92A ARG* 2.9 49.2 + - - +
150A PHE* 2.7 31.2 + + + +
151A ASP 3.2 8.7 - - - +
153A LEU* 1.3 73.9 - - + +
155A ALA* 1.3 56.8 + - - +
156A THR 2.8 7.1 + - - -
157A ALA* 4.3 2.7 - - - -
158A PHE* 2.9 40.5 + + - +
163A LEU 4.4 5.4 - - - +
164A ALA* 3.7 9.9 - - - +
312A THR* 4.9 6.7 - - + +
314A TYR* 3.1 25.2 + - - -
319A LEU* 3.1 33.9 - - + +
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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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151A ASP 2.5 21.1 + - - +
152A TYR* 3.0 17.9 + - + +
154A HIS* 1.3 71.9 - - - +
156A THR* 1.3 55.6 + - - +
159A GLN* 3.6 11.0 - - - -
164A ALA* 3.7 23.6 - - - +
166A THR* 6.6 0.2 - - + -
241A ILE* 5.2 2.9 - - + -
5E VAL 4.6 14.6 - - - +
6E THR* 5.5 1.3 - - + -
7E VAL* 2.7 28.6 + - + +
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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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152A TYR 3.0 9.4 + - - +
153A LEU 3.4 8.3 - - - +
154A HIS 3.0 0.4 - - - -
155A ALA* 1.3 75.4 - - - +
157A ALA* 1.3 75.8 + - - +
158A PHE 3.1 1.9 + - - -
159A GLN* 3.4 25.5 + - - +
237A THR 3.6 5.0 - - - +
239A SER* 3.1 35.3 + - - +
240A GLU 3.3 13.3 + - - -
241A ILE* 4.2 9.2 - - + -
421A ALA* 4.5 4.5 - - + -
422A LEU 4.1 14.8 - - - +
7E VAL* 3.5 20.5 - - - +
18G LEU* 5.5 0.2 - - - +
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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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153A LEU* 2.7 23.0 + - + +
154A HIS* 4.0 4.3 - - - +
156A THR* 1.3 81.6 - - - +
158A PHE* 1.3 59.3 + - + +
236A PHE* 2.9 44.4 - - + -
237A THR 3.0 14.5 + - - -
319A LEU* 4.1 15.5 - - + -
421A ALA* 3.7 15.5 - - + -
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Residues in contact with PHE 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A HIS* 2.9 33.4 + + - +
157A ALA* 1.3 81.0 - - + +
159A GLN* 1.3 71.5 + - - +
161A THR* 2.8 29.1 + - - +
163A LEU* 3.8 17.5 - - + -
164A ALA* 3.8 12.3 - - - +
234A CYS* 4.2 16.2 - - + -
235A ARG 3.5 20.0 - - - +
236A PHE* 4.1 13.9 - + + -
314A TYR* 4.7 2.0 - + - -
317A THR* 3.4 41.7 - - + -
318A GLY 3.6 13.7 - - - -
319A LEU* 3.5 26.2 - - + -
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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