Contacts of the helix formed by residues 1268 - 1275 (chain B) in PDB entry 1AIS
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 GLN1268 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1256B TYR* 3.4 36.1 + - + +
1267B THR* 1.3 73.1 - - - +
1269B ARG* 1.3 57.2 + - - +
1271B VAL* 4.0 1.5 - - - +
1272B ALA* 2.8 33.4 + - - +
1279B GLU* 4.2 15.1 + - + +
1282B VAL* 4.4 17.3 - - + +
1283B ARG* 3.1 40.7 + - - +
1286B TYR* 3.6 29.8 - - - -
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Residues in contact with ARG1269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1267B THR* 3.0 9.7 + - - +
1268B GLN* 1.3 81.0 - - - +
1270B GLU* 1.3 62.5 + - + +
1272B ALA* 3.8 0.5 - - - +
1273B GLU* 3.1 57.5 + - + +
1279B GLU* 3.7 34.4 + - - +
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Residues in contact with GLU1270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1219B LEU* 3.8 6.7 - - + +
1265B LYS 5.0 0.5 - - - +
1266B ARG* 3.5 28.2 + - + +
1267B THR* 2.9 48.3 + - - +
1269B ARG* 1.3 76.6 - - + +
1271B VAL* 1.3 63.0 + - - +
1273B GLU* 3.5 9.4 + - - +
1274B VAL* 3.3 27.2 + - - +
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Residues in contact with VAL1271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1219B LEU* 4.5 10.8 - - + -
1252B ALA* 3.0 41.1 - - + +
1255B LEU* 4.4 9.2 - - + -
1256B TYR* 4.2 24.7 - - + +
1266B ARG* 4.0 23.6 - - + -
1267B THR 3.0 14.2 + - - +
1268B GLN* 4.0 3.6 - - - +
1270B GLU* 1.3 74.5 - - - +
1272B ALA* 1.3 64.5 + - - +
1274B VAL* 3.3 9.3 + - + +
1275B ALA* 3.1 23.0 + - + +
1282B VAL* 5.1 2.9 - - + -
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Residues in contact with ALA1272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1268B GLN 2.8 23.5 + - - +
1269B ARG 3.8 4.0 - - - +
1271B VAL* 1.3 72.8 - - - +
1273B GLU* 1.3 60.4 + - + +
1276B ARG* 2.8 23.9 + - - -
1277B VAL* 3.0 32.3 + - - +
1278B THR 3.9 9.4 - - - +
1279B GLU* 4.0 9.9 - - + +
1282B VAL* 3.9 20.4 - - + +
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Residues in contact with GLU1273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1269B ARG* 3.1 53.7 + - + +
1270B GLU* 3.9 8.3 - - - +
1271B VAL 3.2 0.4 - - - -
1272B ALA* 1.3 79.1 - - + +
1274B VAL* 1.3 66.3 + - + +
1276B ARG* 3.6 20.0 + - - +
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Residues in contact with VAL1274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1215B PHE* 3.5 21.4 - - + -
1218B GLU* 4.0 35.3 - - + +
1219B LEU* 3.5 48.2 - - + -
1255B LEU* 5.7 0.2 - - + -
1270B GLU 3.3 4.4 + - - +
1271B VAL* 3.3 11.9 + - + +
1273B GLU* 1.3 78.5 - - + +
1275B ALA* 1.3 66.8 + - + +
1276B ARG* 3.4 24.6 + - - +
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Residues in contact with ALA1275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1171B THR* 5.0 3.8 - - - +
1215B PHE* 3.9 27.6 - - + -
1248B ALA* 3.6 27.0 - - + +
1252B ALA* 3.7 26.7 - - + -
1271B VAL* 3.1 13.6 + - + +
1272B ALA 4.2 2.2 - - - +
1274B VAL* 1.3 79.7 - - + +
1276B ARG* 1.3 69.6 + - - +
1277B VAL* 4.3 4.0 - - + -
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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