Contacts of the helix formed by residues 1419 - 1433 (chain A) in PDB entry 1FP7
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 GLY1419 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1080A GLY 4.7 4.3 - - - -
1081A LEU* 5.1 1.8 - - - -
1084A ALA* 3.4 17.7 - - - +
1407A ALA* 5.0 2.2 - - - -
1409A SER* 4.2 12.7 - - - +
1415A GLY 3.9 2.4 + - - -
1416A GLY 3.1 8.9 + - - -
1418A GLY* 1.3 77.4 - - - +
1420A LEU* 1.3 58.4 + - - +
1421A GLU 3.3 2.2 - - - -
1422A LEU* 3.3 15.2 + - - +
1423A ALA* 2.9 24.6 + - - +
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Residues in contact with LEU1420 (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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1084A ALA* 4.2 7.9 - - + +
1087A ARG* 4.3 15.5 - - + +
1088A LEU* 3.5 41.1 - - + +
1416A GLY 2.9 31.8 + - - +
1417A GLU* 3.2 29.4 + - + +
1419A GLY* 1.3 77.9 - - - +
1421A GLU* 1.3 63.4 + - - +
1423A ALA* 3.2 3.5 + - - +
1424A ARG* 2.9 41.2 + - - +
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Residues in contact with GLU1421 (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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1396A TYR* 6.1 0.2 - - - -
1404A ALA 4.9 0.2 - - - +
1405A GLU* 2.5 43.6 - - + +
1406A VAL* 3.7 33.0 + - - +
1418A GLY 4.7 2.4 + - - +
1419A GLY 3.3 0.2 - - - -
1420A LEU* 1.3 78.7 - - - +
1422A LEU* 1.3 54.0 + - - +
1424A ARG* 2.8 30.5 + - - +
1425A LYS* 3.0 13.4 + - + +
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Residues in contact with LEU1422 (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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1077A THR* 3.8 20.6 - - + -
1081A LEU* 4.2 21.8 - - + +
1329A VAL* 3.9 24.5 - - + -
1378A VAL* 4.0 3.1 - - + -
1379A VAL 3.9 12.6 - - - +
1380A ALA* 3.8 21.5 - - + -
1405A GLU* 2.8 43.5 + - + +
1406A VAL 5.1 1.5 + - - +
1407A ALA* 4.3 14.4 - - + -
1409A SER* 6.3 0.2 - - - -
1419A GLY* 3.3 15.1 + - - +
1421A GLU* 1.3 77.7 - - - +
1423A ALA* 1.3 60.5 + - - +
1426A VAL* 3.0 25.7 + - - +
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Residues in contact with ALA1423 (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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1081A LEU* 4.2 6.9 - - + +
1084A ALA* 4.0 14.8 - - + -
1085A LEU* 3.9 20.1 - - + +
1088A LEU* 3.3 20.4 - - + -
1419A GLY 2.9 14.3 + - - +
1420A LEU 3.3 9.4 - - - +
1422A LEU* 1.3 75.5 - - - +
1424A ARG* 1.3 64.0 + - - +
1426A VAL* 3.2 3.2 + - - +
1427A LEU* 3.1 29.2 + - - +
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Residues in contact with ARG1424 (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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1088A LEU* 3.7 35.3 - - + +
1420A LEU* 2.9 29.4 + - - +
1421A GLU* 2.8 17.8 + - - +
1423A ALA* 1.3 72.6 - - - +
1425A LYS* 1.3 59.4 + - + +
1427A LEU* 3.8 10.2 + - + +
1428A GLN* 3.2 26.6 + - - +
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Residues in contact with LYS1425 (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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1378A VAL* 4.8 4.9 - - + -
1403A GLY* 5.0 6.6 - - - -
1404A ALA 3.2 30.3 + - - +
1405A GLU* 3.0 38.6 - - - +
1421A GLU* 3.0 14.0 + - + +
1424A ARG* 1.3 77.0 - - + +
1426A VAL* 1.3 64.7 + - - +
1428A GLN* 3.1 25.3 - - + +
1429A THR* 3.1 29.4 + - + +
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Residues in contact with VAL1426 (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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1060A ILE* 4.4 23.8 - - + -
1081A LEU* 4.4 9.9 - - + -
1085A LEU* 5.4 3.8 - - + -
1327A ALA* 5.0 5.8 - - + -
1329A VAL* 3.6 29.4 - - + -
1378A VAL* 4.6 9.0 - - + -
1422A LEU* 3.0 28.5 + - + +
1423A ALA* 3.2 6.0 + - - +
1425A LYS* 1.3 74.1 - - - +
1427A LEU* 1.3 54.2 + - + +
1428A GLN 2.9 3.6 - - - -
1429A THR* 3.1 8.0 + - - -
1430A LEU* 2.6 56.5 + - + +
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Residues in contact with LEU1427 (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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1085A LEU* 4.0 18.2 - - + -
1088A LEU* 3.7 26.2 - - + -
1090A LYS* 3.8 29.6 - - - -
1297A TYR* 3.8 25.6 - - + +
1423A ALA 3.1 19.1 - - - +
1424A ARG* 3.9 9.9 - - + +
1426A VAL* 1.3 79.7 - - - +
1428A GLN* 1.3 56.6 + - - +
1430A LEU* 3.4 10.6 - - + +
1431A GLU* 2.9 35.7 + - - +
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Residues in contact with GLN1428 (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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1424A ARG* 3.2 16.4 + - - +
1425A LYS* 3.1 34.8 - - - +
1426A VAL 2.9 0.4 - - - -
1427A LEU* 1.3 76.4 - - - +
1429A THR* 1.3 66.6 - - + +
1430A LEU 3.1 1.1 - - - -
1431A GLU* 3.2 6.0 + - - +
1432A SER* 2.9 29.6 + - - +
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Residues in contact with THR1429 (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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1327A ALA* 4.4 6.4 - - - +
1376A PRO* 4.2 14.5 - - - +
1377A ALA 5.1 0.2 - - - +
1378A VAL* 3.7 25.1 - - + +
1403A GLY* 5.6 7.0 - - - +
1425A LYS* 3.1 17.1 + - + +
1426A VAL 3.4 5.5 + - - -
1428A GLN* 1.3 79.5 - - + +
1430A LEU* 1.3 60.5 + - - +
1431A GLU 3.1 0.2 - - - -
1432A SER* 3.9 7.0 - - - -
1433A ARG* 2.8 63.2 + - - +
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Residues in contact with LEU1430 (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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1058A LYS* 4.1 25.6 + - + -
1060A ILE* 4.7 7.0 - - + -
1085A LEU* 6.5 0.2 - - + -
1297A TYR* 3.5 36.6 - - + +
1326A ASP* 3.6 39.7 - - + +
1327A ALA* 3.9 13.5 - - + -
1426A VAL* 2.6 30.8 + - + +
1427A LEU* 3.4 15.3 - - + +
1428A GLN 3.1 0.2 - - - -
1429A THR* 1.3 79.1 + - - +
1431A GLU* 1.3 57.0 + - - +
1433A ARG 4.7 6.0 - - - +
1434A PRO* 5.2 4.3 - - - +
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Residues in contact with GLU1431 (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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1427A LEU* 2.9 17.9 + - - +
1428A GLN* 3.5 6.1 - - - +
1429A THR 3.1 0.4 - - - -
1430A LEU* 1.3 79.1 - - - +
1432A SER* 1.3 59.9 + - - +
1433A ARG 3.7 0.2 - - - -
1434A PRO* 4.9 4.5 - - - +
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Residues in contact with SER1432 (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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1428A GLN* 2.9 20.0 + - - +
1429A THR* 3.9 3.3 - - - -
1431A GLU* 1.3 77.1 - - - +
1433A ARG* 1.3 68.2 + - - +
1434A PRO* 3.1 15.2 - - - +
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Residues in contact with ARG1433 (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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1326A ASP 4.3 2.4 - - - +
1375A VAL 5.1 0.2 + - - -
1376A PRO* 3.4 50.5 - - + +
1377A ALA 4.1 16.0 + - - +
1401A LYS 4.7 13.3 + - - -
1402A ALA* 4.9 4.4 - - - +
1403A GLY 5.2 1.4 - - - +
1429A THR* 2.8 43.7 + - - +
1430A LEU* 4.7 2.1 - - - -
1432A SER* 1.3 81.7 - - - +
1434A PRO* 1.3 66.7 - - - +
1435A SER 3.8 0.3 + - - -
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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