Contacts of the helix formed by residues 179 - 188 (chain D) in PDB entry 1MA1
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 VAL 179 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D TYR* 2.8 23.4 + - + +
177D ARG* 3.2 1.1 - - + -
178D ASN* 1.3 95.6 - - - +
180D ARG* 1.3 63.3 + - - +
181D PRO* 3.2 9.6 - - + -
182D ASP* 3.0 47.5 + - + +
183D TYR 3.6 3.3 + - - -
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Residues in contact with ARG 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C TRP* 6.1 0.4 - - - -
123D ALA 3.3 9.9 + - - -
124D ILE* 3.0 32.7 + - + +
126D ALA* 2.9 26.1 + - - +
128D GLY* 3.2 23.2 + - - +
167D VAL* 3.1 47.0 + - + +
169D GLU* 4.6 6.3 + - - +
172D TYR* 2.9 43.3 + - + +
178D ASN 2.8 11.6 + - - +
179D VAL* 1.3 71.4 - - - +
181D PRO* 1.3 63.7 - - + +
183D TYR* 3.2 4.6 + - + +
184D VAL* 2.9 30.2 + - + +
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Residues in contact with PRO 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D ILE* 3.8 41.7 - - + +
178D ASN 4.7 0.9 - - - +
179D VAL* 3.2 12.3 - - + -
180D ARG* 1.3 95.6 - - + +
182D ASP* 1.3 58.2 + - - +
184D VAL* 3.4 1.8 + - + +
185D GLU* 2.9 29.8 + - - +
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Residues in contact with ASP 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D TYR* 3.5 25.1 - - + -
179D VAL* 3.0 30.8 + - + +
181D PRO* 1.3 77.9 - - - +
183D TYR* 1.3 58.7 + - - +
185D GLU* 3.4 6.7 + - - +
186D ALA* 2.9 29.1 + - - +
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Residues in contact with TYR 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D HIS 5.4 0.2 - - - -
24D ILE* 4.3 22.1 - - + +
28D GLN* 6.3 0.2 - - + -
83D PHE* 3.4 24.1 - - - -
165D LEU* 3.7 16.8 - - + +
166D ASP 2.9 29.5 + - - -
167D VAL* 4.7 3.6 - - + -
171D ALA* 3.5 27.3 + - + +
172D TYR* 3.2 35.9 - + + -
176D TYR* 3.6 34.4 - + + -
179D VAL 3.6 2.2 + - - -
180D ARG 3.2 10.6 + - - +
182D ASP* 1.3 75.4 - - - +
184D VAL* 1.3 74.1 + - + +
186D ALA* 3.2 4.4 + - + +
187D PHE* 3.0 23.8 + + + +
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Residues in contact with VAL 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D SER* 3.7 38.6 - - - +
123D ALA* 3.8 21.3 - - + -
124D ILE* 3.9 16.4 - - + -
165D LEU* 4.3 13.2 - - + -
167D VAL* 4.4 2.0 - - + -
180D ARG* 2.9 26.3 + - + +
181D PRO 3.8 4.3 - - - +
183D TYR* 1.3 87.0 - - + +
185D GLU* 1.3 63.3 + - - +
187D PHE* 3.3 14.9 - - - +
188D TRP* 3.1 18.0 + - - +
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Residues in contact with GLU 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D ARG* 2.7 40.8 + - - -
120D SER* 5.6 0.5 + - - -
181D PRO 2.9 18.6 + - - +
182D ASP* 3.5 8.1 - - - +
183D TYR 3.2 0.2 - - - -
184D VAL* 1.3 76.3 - - - +
186D ALA* 1.3 64.9 + - - +
187D PHE 3.2 0.7 + - - -
188D TRP* 3.4 13.9 + - - +
189D ASN* 3.7 9.2 + - - +
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Residues in contact with ALA 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D HIS* 4.0 26.3 - - + +
24D ILE* 6.2 0.7 - - + -
176D TYR* 3.2 27.6 - - + +
182D ASP 2.9 14.6 + - - +
183D TYR* 3.2 6.0 + - + +
185D GLU* 1.3 76.4 - - - +
187D PHE* 1.3 63.3 + - - +
189D ASN* 3.0 31.0 + - - +
190D ILE* 4.0 1.6 + - - +
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Residues in contact with PHE 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ILE* 5.7 2.0 - - + -
83D PHE* 4.0 5.4 - + - -
86D ASN* 4.2 2.7 - - - -
87D MET* 3.8 36.8 - - + -
119D PHE* 4.5 7.4 - + - -
163D LEU* 4.0 17.3 - - + -
164D VAL 3.8 17.0 - - - -
165D LEU* 3.5 47.3 - - + -
183D TYR* 3.0 15.3 + + + +
184D VAL 3.3 12.1 - - - +
185D GLU 3.1 0.4 - - - -
186D ALA* 1.3 78.0 - - - +
188D TRP* 1.3 73.1 + + - +
190D ILE* 2.9 31.0 + - + +
191D VAL* 3.2 28.2 + - + +
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Residues in contact with TRP 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D GLY* 3.3 18.5 - - - -
95D GLY 4.2 6.2 + - - +
112D PHE* 4.5 6.1 - + - -
115D PHE* 3.8 20.6 - + - -
116D ARG* 3.5 70.5 - - + +
119D PHE* 3.6 35.9 - + + -
120D SER* 3.1 18.8 + - - -
163D LEU* 4.7 2.9 - - + -
184D VAL* 3.1 30.2 + - + +
185D GLU* 3.4 8.7 + - - +
186D ALA 3.1 0.8 + - - -
187D PHE* 1.3 84.4 - + - +
189D ASN* 1.3 60.6 + - - +
190D ILE 3.3 0.2 - - - -
191D VAL* 3.6 22.1 - - + +
193D TRP* 3.8 27.8 + + - -
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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