Contacts of the helix formed by residues 1181 - 1191 (chain D) in PDB entry 2BAP
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 VAL1181 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217B ASN 2.9 9.7 + - - -
218B ASN* 3.5 27.4 - - + +
219B LYS* 3.8 18.2 - - + +
222B ILE* 4.0 19.5 - - + -
1180D GLY* 1.3 72.6 - - - +
1182D MET* 1.3 55.6 + - - +
1183D ASP 3.0 4.3 - - - -
1184D SER* 2.7 40.3 + - - -
1185D LEU* 3.7 11.0 + - + -
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Residues in contact with MET1182 (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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213B LYS* 4.4 12.3 - - + +
216B MET* 4.0 15.9 - - - +
217B ASN* 3.4 26.7 - - - +
222B ILE* 5.0 5.2 - - + -
252B LYS* 4.6 1.3 - - + +
253B LEU* 3.7 33.2 - - + +
256B ALA* 3.6 18.8 - - + -
257B LEU* 6.4 0.4 - - - -
1181D VAL* 1.3 79.4 - - + +
1183D ASP* 1.3 58.5 + - - +
1184D SER 3.3 0.4 - - - -
1185D LEU* 3.7 27.6 - - + -
1186D LEU* 3.3 46.2 + - + +
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Residues in contact with ASP1183 (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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213B LYS* 2.8 31.4 + - - -
217B ASN* 3.0 24.9 + - - +
1180D GLY* 4.6 9.0 - - - +
1181D VAL 2.8 1.0 + - - +
1182D MET* 1.3 77.0 - - - +
1184D SER* 1.3 64.0 + - - +
1186D LEU* 3.8 5.4 + - - +
1187D GLU* 3.3 23.0 + - - +
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Residues in contact with SER1184 (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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1180D GLY 3.8 10.1 + - - -
1181D VAL* 2.7 16.8 + - - -
1183D ASP* 1.3 75.9 - - - +
1185D LEU* 1.3 68.4 + - - -
1187D GLU* 3.2 10.7 + - - +
1188D ALA* 3.1 20.8 + - - +
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Residues in contact with LEU1185 (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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222B ILE* 4.9 4.9 - - + -
256B ALA* 4.0 14.4 - - + +
259B ILE* 4.5 19.3 - - + +
260B LEU* 3.7 32.5 - - + +
261B PRO* 5.9 4.0 - - + -
1181D VAL* 3.7 13.4 + - + +
1182D MET* 3.7 34.5 - - + +
1183D ASP 3.4 0.4 - - - -
1184D SER* 1.3 81.1 - - - +
1186D LEU* 1.3 62.6 + - - +
1188D ALA* 3.0 20.4 + - + +
1189D LEU* 3.2 17.2 + - - +
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Residues in contact with LEU1186 (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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213B LYS* 3.8 26.5 - - - +
252B LYS* 3.5 55.0 - - + +
256B ALA* 4.5 1.8 - - + -
307B GLN* 4.9 1.5 + - - +
1182D MET* 3.3 35.1 + - + +
1183D ASP* 4.1 6.3 - - - +
1184D SER 3.3 0.4 - - - -
1185D LEU* 1.3 78.3 - - - +
1187D GLU* 1.3 62.5 + - - +
1189D LEU* 3.2 28.3 + - + +
1190D GLN* 3.5 11.8 + - - +
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Residues in contact with GLU1187 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1183D ASP 3.3 13.0 + - - +
1184D SER* 3.2 14.2 + - - +
1186D LEU* 1.3 74.9 - - - +
1188D ALA* 1.3 57.9 + - - +
1189D LEU 3.0 9.0 + - - -
1190D GLN* 5.0 0.6 - - - +
1191D SER* 3.3 31.3 + - - +
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Residues in contact with ALA1188 (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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1184D SER 3.1 10.9 + - - +
1185D LEU* 3.0 15.3 + - + +
1187D GLU* 1.3 74.8 - - - +
1189D LEU* 1.3 57.5 + - - +
1191D SER 3.7 7.9 - - - -
1192D GLY* 3.4 2.9 - - - -
1193D ALA* 3.1 25.7 + - + +
1194D ALA* 3.2 34.0 + - + +
1195D PHE* 4.2 1.2 - - - -
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Residues in contact with LEU1189 (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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255B SER* 4.1 9.4 - - - +
256B ALA* 4.0 17.3 - - - +
259B ILE* 3.6 34.8 - - + -
307B GLN* 3.3 37.0 - - + +
311B ALA* 4.7 2.9 - - + -
352B GLN* 2.9 17.7 + - - -
1185D LEU 3.2 5.3 + - - +
1186D LEU* 3.4 29.4 - - + +
1187D GLU 3.0 1.2 - - - -
1188D ALA* 1.3 79.0 - - - +
1190D GLN* 1.3 64.1 + - - +
1192D GLY 3.6 6.6 + - - -
1195D PHE* 3.6 35.9 - - + -
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Residues in contact with GLN1190 (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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252B LYS* 4.7 22.0 - - - +
300B ALA 5.9 0.6 + - - -
303B VAL* 4.3 19.1 - - + +
307B GLN* 3.4 17.8 + - - +
348B ASP* 2.9 41.9 - - - +
351B VAL* 3.3 23.9 - - - +
352B GLN* 3.7 5.3 + - - +
1186D LEU 3.5 10.1 + - - +
1187D GLU* 5.0 0.4 - - - +
1189D LEU* 1.3 78.0 - - - +
1191D SER* 1.3 60.0 + - - +
1192D GLY 3.3 4.0 + - - -
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Residues in contact with SER1191 (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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348B ASP* 5.0 4.2 + - - -
351B VAL* 4.3 7.0 - - - -
1187D GLU* 3.3 24.5 + - - +
1188D ALA* 3.5 5.0 - - - +
1190D GLN* 1.3 74.6 - - - +
1192D GLY* 1.3 52.7 + - - +
1193D ALA* 2.8 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