Contacts of the strand formed by residues 1269 - 1273 (chain A) in PDB entry 3AL3
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 ILE1269 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1267A GLN* 3.8 35.9 - - + +
1268A TYR* 1.3 78.7 - - - +
1270A PHE* 1.3 61.3 + - - +
1293A LEU* 3.5 30.1 - - + -
1295A ILE* 3.6 34.8 - - + -
1303A THR* 4.0 27.1 - - + +
1304A CYS* 3.4 6.6 - - - -
1305A THR* 2.7 38.2 + - + +
1306A HIS 3.1 5.9 + - - +
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Residues in contact with PHE1270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1268A TYR* 3.6 23.6 - + + -
1269A ILE* 1.3 75.9 - - - +
1271A GLN* 1.3 66.3 + - - +
1272A LEU* 4.9 0.2 - - + -
1287A ILE* 3.6 28.9 - - + -
1293A LEU 2.7 16.8 + - - +
1294A VAL* 3.3 5.3 - - + -
1295A ILE* 2.8 32.7 + - - +
1304A CYS* 4.2 0.9 - - - -
1306A HIS* 3.2 35.2 - + + -
1308A VAL* 3.9 28.5 - - + -
1329A LEU* 4.6 0.7 - - + -
1333A TYR* 4.0 21.1 - + - -
1334A LEU* 4.3 5.8 - - + -
1343A PHE* 3.5 37.2 - + - -
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Residues in contact with GLN1271 (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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1270A PHE* 1.3 77.8 - - - +
1272A LEU* 1.3 70.5 + - - +
1294A VAL* 4.7 0.4 - - - -
1295A ILE* 3.4 39.8 + - + +
1297A LYS* 3.9 4.4 + - - +
1299A CYS 2.9 22.6 + - - -
1300A PHE* 3.4 16.8 - - - -
1301A ASP* 2.9 31.9 + - - +
1304A CYS* 3.9 14.0 - - + +
1306A HIS 3.0 8.5 + - - -
1307A ILE* 3.2 19.1 - - + +
1308A VAL 3.2 22.0 + - - -
1317A LYS* 3.9 13.4 - - + +
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Residues in contact with LEU1272 (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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1270A PHE* 4.9 0.7 - - + -
1271A GLN* 1.3 84.0 - - - +
1273A SER* 1.3 61.6 + - - +
1275A LEU* 4.0 14.1 - - + -
1280A ARG* 3.3 50.5 + - + +
1283A TYR* 4.4 13.9 - - + -
1284A CYS* 4.1 16.8 - - - +
1287A ILE* 4.3 19.3 - - + -
1294A VAL* 4.1 11.6 - - + +
1295A ILE 4.9 1.8 + - - -
1307A ILE* 4.5 0.4 - - - -
1308A VAL* 3.5 25.4 - - + -
1317A LYS* 2.9 28.8 + - - +
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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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1272A LEU* 1.3 75.8 - - - +
1274A SER* 1.3 77.2 + - - +
1275A LEU* 3.3 7.0 + - - +
1280A ARG* 3.9 1.7 - - - +
1307A ILE* 3.9 20.4 - - - -
1308A VAL 3.1 5.1 + - - -
1309A VAL* 3.4 13.4 - - - +
1310A GLY 3.0 13.7 + - - -
1315A ASN* 3.4 18.5 + - - -
1317A LYS* 3.9 3.9 - - - +
1318A TYR* 4.9 1.3 + - - +
1133B TPO 2.7 26.7 + - - -
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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