Contacts of the helix formed by residues 1270 - 1276 (chain A) in PDB entry 3PTA
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 ASN1270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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701A ASP* 3.1 34.8 + - - +
704A GLU* 2.7 38.8 + - - +
706A ASP* 2.6 25.5 - - - +
1232A MET* 5.2 1.8 - - - -
1268A VAL* 3.4 1.4 - - - +
1269A ARG* 1.3 80.3 + - - +
1271A PHE* 1.3 58.1 + - - +
1272A VAL 3.1 1.3 - - - -
1273A SER* 3.2 10.6 + - - +
1274A PHE* 3.0 54.0 + - + -
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Residues in contact with PHE1271 (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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1226A CYS* 4.4 12.8 - - - -
1248A VAL* 4.5 13.0 - - + -
1265A LEU* 4.3 13.7 - - + -
1267A ASN* 4.2 25.4 - - + -
1268A VAL* 3.2 20.5 + - + +
1269A ARG 2.6 5.1 + - - -
1270A ASN* 1.3 75.1 - - - +
1272A VAL* 1.3 58.3 + - - +
1273A SER 3.1 4.1 + - - -
1274A PHE* 3.4 21.2 + + + -
1279A VAL* 3.4 33.6 - - + +
1280A LEU* 3.8 28.5 + - + +
1283A THR* 4.1 22.0 - - + -
1313A ALA* 4.0 6.7 - - + -
1315A ILE* 3.8 31.2 - - + -
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Residues in contact with VAL1272 (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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1269A ARG* 3.2 40.4 - - - +
1271A PHE* 1.3 76.9 - - - +
1273A SER* 1.3 58.4 + - - +
1277A SER* 3.2 19.7 + - - -
1280A LEU* 3.6 33.4 - - + +
1296A PHE* 4.6 10.1 - - + -
1297A GLY 5.0 1.3 - - - +
1298A VAL* 4.5 10.5 - - + -
1313A ALA* 4.0 17.7 - - + -
1315A ILE* 6.0 0.4 - - + -
1343A VAL* 3.5 34.5 - - + +
1344A VAL 5.0 0.5 - - - +
1345A VAL* 4.4 1.7 - - - +
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Residues in contact with SER1273 (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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706A ASP* 3.1 27.5 + - - -
1232A MET* 3.7 17.7 - - - +
1269A ARG* 3.8 9.3 + - - -
1270A ASN* 3.3 14.6 + - - -
1272A VAL* 1.3 82.1 - - - +
1274A PHE* 1.3 69.5 + - - +
1275A LYS 3.5 0.2 + - - -
1276A ARG* 3.2 6.9 + - - -
1277A SER* 2.8 21.4 + - - -
1343A VAL* 6.3 0.2 - - - -
1344A VAL 5.8 2.0 - - - -
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Residues in contact with PHE1274 (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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700A ASP* 3.6 37.0 - - + -
701A ASP* 4.1 3.6 - - - -
1226A CYS* 4.2 24.0 - - + -
1229A PHE* 4.6 8.7 - - + +
1230A SER* 3.6 20.4 - - - -
1231A GLY 3.0 18.6 - - - +
1232A MET* 4.1 6.7 - - + -
1268A VAL* 3.7 4.7 - - + -
1270A ASN* 3.0 43.7 + - + -
1271A PHE* 3.4 22.9 + + + +
1273A SER* 1.3 76.0 - - - +
1275A LYS* 1.3 59.2 + - - +
1277A SER* 2.7 25.1 + - - -
1279A VAL* 3.1 29.4 - - + +
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Residues in contact with LYS1275 (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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1229A PHE* 4.3 20.0 - - + +
1231A GLY* 4.0 14.6 + - - +
1232A MET* 3.7 12.1 - - - +
1233A ASN* 3.0 33.5 + - - +
1234A ARG* 3.8 11.0 + - - +
1235A PHE* 3.6 44.9 + - + -
1236A ASN* 4.3 2.4 + - - -
1239A THR* 3.4 40.2 + - - +
1273A SER 3.5 0.2 + - - -
1274A PHE* 1.3 71.6 - - - +
1276A ARG* 1.3 65.0 + - - +
1278A MET* 2.9 20.3 - - - +
1279A VAL* 3.8 8.5 - - + -
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Residues in contact with ARG1276 (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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1232A MET* 3.3 30.2 + - - +
1233A ASN* 3.8 10.3 - - - +
1234A ARG* 3.8 30.3 - - + +
1235A PHE 5.7 0.2 - - - +
1273A SER 3.2 5.9 + - - -
1274A PHE 3.1 1.0 - - - -
1275A LYS* 1.3 74.5 - - - +
1277A SER* 1.3 67.7 + - - +
1278A MET* 2.9 12.9 + - + +
1281A LYS* 4.3 10.0 + - - -
1346A ASP* 5.0 10.2 - - - +
5B G 5.6 4.8 + - - -
6B T 3.5 23.2 + - - -
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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