Contacts of the helix formed by residues 1362 - 1370 (chain A) in PDB entry 5FLM
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 ILE1362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1126A GLU 5.3 1.1 - - - +
1127A LEU* 3.7 32.5 - - + +
1130A ILE* 4.9 9.6 - - + -
1360A ASN 4.1 9.4 - - - +
1361A ASP* 1.3 78.8 + - - +
1363A VAL* 1.3 60.0 + - + +
1365A ILE* 3.1 12.6 + - + +
1366A PHE* 2.9 22.0 + - - +
1374A VAL* 3.5 32.7 - - + +
1377A ALA* 5.8 0.9 - - + -
1378A LEU* 3.6 42.2 - - + +
1381A GLU* 5.4 1.3 - - + -
1411A LEU* 3.7 20.4 - - + -
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Residues in contact with VAL1363 (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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1130A ILE* 4.0 27.8 - - + +
1131A SER 4.5 13.9 - - - +
1132A LYS* 4.7 26.7 - - + +
1361A ASP* 3.4 8.1 + - - +
1362A ILE* 1.3 76.3 - - + +
1364A GLU* 1.3 59.1 + - + +
1366A PHE* 2.7 28.7 + - + +
1367A THR* 2.9 29.3 + - + +
1411A LEU* 4.1 6.3 - - + -
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Residues in contact with GLU1364 (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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1137A PRO* 5.4 1.7 - - - +
1303A GLN* 5.4 1.2 - - - +
1341A VAL* 3.1 47.6 - - - +
1342A SER* 5.3 2.5 - - - -
1343A LEU* 3.4 17.2 - - + +
1359A SER* 4.7 3.8 - - - +
1361A ASP* 3.1 31.8 + - + +
1362A ILE 3.3 0.4 - - - -
1363A VAL* 1.3 78.9 - - + +
1365A ILE* 1.3 58.5 + - - +
1367A THR* 4.1 8.1 - - - +
1368A VAL* 3.3 27.5 - - + +
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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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1343A LEU* 4.2 11.4 - - + -
1358A THR* 4.4 6.5 - - + -
1359A SER* 3.1 38.1 - - - +
1360A ASN 4.8 1.3 - - - +
1361A ASP 3.2 16.5 + - - +
1362A ILE* 3.1 10.2 + - - +
1363A VAL 3.1 0.4 - - - -
1364A GLU* 1.3 78.7 - - - +
1366A PHE* 1.3 59.0 + - - +
1369A LEU* 2.9 29.8 + - + +
1370A GLY 3.2 4.0 + - - -
1373A ALA* 3.6 39.9 - - + +
1374A VAL* 3.9 3.8 - - + +
1377A ALA* 3.6 23.1 - - + -
144E LEU* 4.5 4.0 - - + -
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Residues in contact with PHE1366 (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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1362A ILE 2.9 7.5 + - - +
1363A VAL* 2.7 21.8 + - + +
1365A ILE* 1.3 72.2 - - - +
1367A THR* 1.3 72.2 + - + +
1368A VAL 3.0 1.8 + - - -
1370A GLY* 2.9 27.1 + - - -
1371A ILE* 3.6 44.2 - - + -
1374A VAL* 3.5 18.6 - - + -
1409A GLY 4.5 0.9 - - - -
1410A HIS* 4.1 20.9 - - + -
1411A LEU* 4.1 19.1 - - + -
174E GLN* 3.4 30.5 - - + -
177E ASP* 5.7 3.4 - - - -
178E PRO* 4.3 6.9 - - + +
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Residues in contact with THR1367 (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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1363A VAL* 2.9 28.0 + - + +
1364A GLU* 4.1 5.5 - - - -
1366A PHE* 1.3 88.7 - - + +
1368A VAL* 1.3 68.0 + - - +
178E PRO* 3.8 14.7 - - - +
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Residues in contact with VAL1368 (chain A).
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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1343A LEU* 4.2 9.0 - - + -
1344A MET* 3.5 47.3 - - + +
1347A LEU* 4.1 19.5 - - + -
1364A GLU* 3.3 22.4 + - + +
1365A ILE 3.6 0.4 + - - -
1366A PHE 3.0 0.8 + - - -
1367A THR* 1.3 88.3 - - - +
1369A LEU* 1.3 70.3 + - + +
1370A GLY 3.4 0.7 - - - -
139E ILE* 4.0 11.9 - - + +
178E PRO* 3.4 22.3 - - - +
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Residues in contact with LEU1369 (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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1343A LEU* 4.6 11.9 - - + -
1347A LEU* 4.6 8.1 - - + -
1357A THR 5.2 0.7 - - - +
1358A THR* 6.3 0.7 - - - -
1365A ILE* 2.9 17.1 + - + +
1368A VAL* 1.3 86.5 - - + +
1370A GLY* 1.3 59.7 + - - +
1372A GLU* 5.0 0.9 + - - +
1373A ALA* 3.5 25.7 + - + +
137E ILE* 6.1 0.9 - - + -
139E ILE* 3.7 35.4 - - + +
142E HIS* 3.8 51.1 - - + +
144E LEU* 4.4 4.3 - - + -
145E VAL* 3.7 16.7 - - + +
178E PRO* 4.9 0.7 - - - -
179E VAL* 3.8 14.5 - - - +
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Residues in contact with GLY1370 (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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1365A ILE 3.2 1.5 + - - +
1366A PHE* 2.9 23.6 + - - -
1368A VAL 3.4 1.4 - - - -
1369A LEU* 1.3 80.7 - - - +
1371A ILE* 1.3 61.7 - - - -
1372A GLU 3.4 2.7 - - - -
1373A ALA* 4.2 0.4 - - - +
1374A VAL* 3.2 26.2 + - - +
177E ASP* 3.1 21.5 - - - -
178E PRO* 4.3 2.0 - - - +
179E VAL* 4.9 1.6 - - - -
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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