Contacts of the strand formed by residues 1360 - 1368 (chain A) in PDB entry 1MFL
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 THR1360 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1284A ARG* 3.1 35.1 - - - +
1285A VAL 3.7 4.2 + - - -
1286A GLU* 4.0 18.6 + - - +
1338A ASN* 3.5 15.2 + - - +
1358A GLN 3.2 9.9 + - - +
1359A ASN* 1.3 80.3 - - + +
1361A VAL* 1.3 58.8 + - - +
1362A GLU* 4.7 15.5 - - + +
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Residues in contact with VAL1361 (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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1283A VAL 3.5 2.9 - - - +
1284A ARG* 3.5 1.9 - - - -
1285A VAL* 2.8 39.4 + - + +
1287A LYS* 4.6 3.6 - - + -
1291A LEU* 4.0 25.6 - - + -
1337A ALA* 4.3 6.7 - - + -
1338A ASN* 3.4 6.5 - - - +
1354A LEU* 4.5 4.9 - - + -
1357A PHE* 3.7 41.3 - - + -
1358A GLN 4.8 0.4 - - - +
1359A ASN 4.3 5.2 - - - +
1360A THR* 1.3 79.4 + - - +
1362A GLU* 1.3 61.8 + - - +
1363A LEU* 3.7 27.6 + - + +
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Residues in contact with GLU1362 (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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1283A VAL 3.7 4.5 - - - -
1284A ARG* 2.7 50.8 + - + +
1336A GLN* 4.5 1.9 - - - +
1337A ALA* 3.5 2.1 + - - -
1338A ASN* 2.8 44.8 + - - +
1339A GLY 4.6 1.2 + - - -
1360A THR* 4.6 11.8 - - + +
1361A VAL* 1.3 73.6 - - - +
1363A LEU* 1.3 63.2 + - - +
1364A ILE* 5.4 0.7 - - - +
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Residues in contact with LEU1363 (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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1282A ARG* 3.3 6.8 - - - +
1283A VAL* 2.7 44.7 + - + +
1285A VAL* 4.2 11.4 - - + -
1291A LEU* 6.3 0.2 - - + -
1293A PHE* 4.2 11.9 - - + -
1328A LEU* 3.9 35.4 - - + -
1334A ILE* 4.3 14.6 - - + -
1336A GLN 3.4 4.5 - - - +
1337A ALA* 3.7 25.4 - - + -
1354A LEU* 4.4 9.2 - - + -
1361A VAL* 3.7 20.0 - - + +
1362A GLU* 1.3 76.0 - - - +
1364A ILE* 1.3 64.2 + - - +
1365A ILE* 4.2 9.9 - - + -
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Residues in contact with ILE1364 (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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1280A GLU* 4.1 17.7 - - + +
1281A ILE 3.4 11.2 - - - +
1282A ARG* 4.5 21.5 - - + +
1334A ILE* 3.8 0.5 - - - -
1335A ILE* 2.9 45.4 + - + +
1336A GLN* 3.0 52.1 + - + +
1362A GLU 5.4 0.9 - - - +
1363A LEU* 1.3 78.3 - - - +
1365A ILE* 1.3 72.2 + - - +
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Residues in contact with ILE1365 (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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1279A MET 3.7 0.3 - - - +
1280A GLU* 3.1 6.9 - - - +
1281A ILE* 2.9 52.3 + - + +
1283A VAL* 4.0 8.3 - - + -
1328A LEU* 3.9 20.9 - - + -
1332A ASP* 3.5 37.7 - - + +
1333A LYS 3.1 11.4 - - - +
1334A ILE* 4.3 17.5 - - + -
1335A ILE* 4.7 0.4 - - - -
1363A LEU* 4.3 11.2 - - + -
1364A ILE* 1.3 79.9 - - - +
1366A VAL* 1.3 61.8 + - - +
1367A ARG* 3.8 26.7 - - + +
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Residues in contact with VAL1366 (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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1278A SER* 3.8 28.0 - - - +
1279A MET 3.4 10.1 - - - +
1280A GLU* 4.4 10.5 - - + +
1331A GLY 4.3 1.9 - - - +
1332A ASP* 3.7 3.1 - - - -
1333A LYS* 2.9 46.7 + - + +
1335A ILE* 3.8 36.1 - - + -
1365A ILE* 1.3 74.8 - - - +
1367A ARG* 1.3 62.5 + - - +
1368A GLU* 4.1 8.1 + - - +
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Residues in contact with ARG1367 (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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1278A SER* 3.3 3.2 - - - -
1279A MET* 2.8 40.4 + - + +
1281A ILE* 3.7 27.7 - - + +
1283A VAL* 5.3 0.4 - - - +
1326A LYS 5.7 1.6 + - - -
1327A LEU 3.0 25.3 + - - -
1328A LEU* 3.9 1.0 - - - +
1329A GLN* 3.5 34.6 + - - +
1332A ASP* 2.9 42.3 + - - +
1365A ILE* 3.8 13.9 - - + +
1366A VAL* 1.3 74.5 - - - +
1368A GLU* 1.3 78.5 + - - +
1369A VAL* 3.8 10.4 + - + -
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Residues in contact with GLU1368 (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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1277A GLY 3.4 10.1 + - - +
1278A SER* 2.6 27.7 + - - -
1307A ARG* 3.4 39.8 + - - +
1329A GLN* 4.8 5.2 + - - -
1331A GLY 5.4 8.9 + - - +
1366A VAL* 4.1 10.6 + - - +
1367A ARG* 1.3 88.1 - - - +
1369A VAL* 1.3 59.7 + - - +
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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