Contacts of the helix formed by residues 1419 - 1433 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1080B GLY 4.2 2.7 - - - -
1081B LEU* 4.7 2.6 - - - +
1084B ALA* 3.3 19.6 - - - +
1407B ALA* 4.2 12.3 - - - -
1409B SER* 3.3 22.1 + - - -
1416B GLY 3.1 8.4 + - - -
1418B GLY* 1.3 73.5 - - - +
1420B LEU* 1.3 62.4 + - - +
1421B GLU 3.6 0.4 - - - -
1422B LEU* 3.6 5.5 + - - +
1423B ALA* 3.1 18.5 + - - +
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Residues in contact with LEU1420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1084B ALA* 4.2 11.9 - - + +
1087B ARG* 4.6 10.3 - - + -
1088B LEU* 4.1 24.5 - - + -
1416B GLY 2.9 30.7 + - - +
1417B GLU* 2.8 29.5 + - + +
1418B GLY 3.0 2.0 - - - -
1419B GLY* 1.3 74.8 - - - +
1421B GLU* 1.3 68.8 + - + +
1423B ALA* 3.0 15.4 + - + +
1424B ARG* 3.3 54.2 + - - +
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Residues in contact with GLU1421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1405B GLU* 3.1 31.5 - - - +
1406B VAL* 3.2 41.2 - - - +
1418B GLY 4.1 4.6 + - - +
1419B GLY 3.6 0.2 - - - -
1420B LEU* 1.3 77.9 - - - +
1422B LEU* 1.3 64.6 + - - +
1424B ARG* 3.5 19.2 + - - +
1425B LYS* 3.5 8.0 + - - +
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Residues in contact with LEU1422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1077B THR* 5.1 6.5 - - + -
1081B LEU* 4.0 18.4 - - + -
1329B VAL* 4.4 11.9 - - + -
1378B VAL* 3.2 34.1 - - + -
1379B VAL 4.0 4.3 - - - +
1380B ALA* 4.2 23.1 - - + -
1405B GLU* 3.7 17.6 - - + +
1406B VAL 4.5 1.2 + - - -
1407B ALA* 4.5 20.4 - - + -
1419B GLY* 3.6 7.2 + - - +
1420B LEU 3.2 0.4 - - - -
1421B GLU* 1.3 76.0 - - - +
1423B ALA* 1.3 62.6 + - - +
1425B LYS* 2.9 4.7 + - + +
1426B VAL* 2.8 46.8 + - + +
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Residues in contact with ALA1423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1081B LEU* 3.8 14.8 - - + +
1084B ALA* 3.8 20.9 - - + +
1085B LEU* 3.9 20.2 - - - +
1088B LEU* 5.2 6.5 - - + -
1419B GLY 3.1 14.0 + - - +
1420B LEU* 3.0 11.3 + - - +
1422B LEU* 1.3 76.5 - - - +
1424B ARG* 1.3 65.7 + - + +
1426B VAL* 3.4 3.9 + - - +
1427B LEU* 3.3 25.9 + - + +
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Residues in contact with ARG1424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088B LEU* 4.6 23.6 - - + +
1420B LEU* 3.3 48.9 + - + +
1421B GLU* 3.8 12.2 - - - +
1422B LEU 3.2 0.6 - - - -
1423B ALA* 1.3 74.5 - - - +
1425B LYS* 1.3 51.8 + - - +
1427B LEU* 3.1 12.6 + - - +
1428B GLN* 2.7 41.9 + - - +
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Residues in contact with LYS1425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1378B VAL* 4.6 6.7 - - + -
1403B GLY* 3.4 31.7 - - - -
1404B ALA 3.8 7.9 + - - +
1405B GLU* 3.8 36.7 + - + +
1421B GLU 3.5 1.7 + - - +
1422B LEU* 2.9 10.2 + - + +
1424B ARG* 1.3 79.6 - - - +
1426B VAL* 1.3 57.3 + - - +
1428B GLN* 3.4 35.9 + - - +
1429B THR* 2.8 45.1 + - + +
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Residues in contact with VAL1426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1060B ILE* 3.7 34.1 - - + -
1081B LEU* 3.9 11.4 - - + -
1085B LEU* 6.2 2.2 - - + -
1327B ALA* 5.1 6.5 - - + +
1329B VAL* 5.1 6.5 - - + -
1378B VAL* 5.0 7.0 - - + -
1422B LEU* 2.8 55.6 + - + +
1423B ALA* 3.5 9.4 - - - +
1424B ARG 3.2 0.2 - - - -
1425B LYS* 1.3 74.5 - - - +
1427B LEU* 1.3 61.7 + - + +
1429B THR* 3.4 6.7 + - - +
1430B LEU* 2.9 38.6 + - + +
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Residues in contact with LEU1427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1085B LEU* 5.1 12.8 - - + +
1088B LEU* 5.7 8.1 - - + -
1090B LYS* 4.2 28.7 - - + +
1297B TYR* 3.9 33.0 - - + +
1423B ALA* 3.3 14.3 + - + +
1424B ARG* 3.1 10.2 + - - +
1426B VAL* 1.3 77.9 - - + +
1428B GLN* 1.3 61.6 + - - +
1430B LEU* 3.5 12.0 - - + -
1431B GLU* 2.9 38.5 + - + +
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Residues in contact with GLN1428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1424B ARG* 2.7 22.1 + - - +
1425B LYS* 3.2 44.9 + - - +
1427B LEU* 1.3 76.9 - - - +
1429B THR* 1.3 59.9 + - + +
1431B GLU* 4.0 12.9 - - - +
1432B SER* 3.0 23.7 + - - -
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Residues in contact with THR1429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1327B ALA* 5.5 2.9 - - - +
1376B PRO* 4.6 10.2 - - - +
1377B ALA 5.2 2.5 - - - +
1378B VAL* 4.0 20.2 - - + +
1403B GLY* 5.0 4.7 - - - +
1425B LYS* 2.8 36.0 + - + +
1426B VAL* 3.4 8.3 + - - +
1428B GLN* 1.3 78.7 - - + +
1430B LEU* 1.3 61.0 + - - +
1431B GLU 3.0 6.1 - - - -
1432B SER* 3.8 6.1 - - - -
1433B ARG* 2.9 46.3 + - - +
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Residues in contact with LEU1430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1058B LYS* 3.3 40.5 - - + +
1059B LEU 4.9 0.2 - - - +
1060B ILE* 4.9 12.1 - - + -
1297B TYR* 5.2 3.6 - - + -
1326B ASP* 2.9 49.6 - - + +
1327B ALA* 4.5 13.0 - - + -
1426B VAL* 2.9 23.6 + - + +
1427B LEU* 3.1 14.3 + - + +
1429B THR* 1.3 75.5 + - - +
1431B GLU* 1.3 56.8 + - - +
1433B ARG 4.3 7.6 - - - +
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Residues in contact with GLU1431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1427B LEU* 2.9 20.7 - - + +
1428B GLN* 4.0 14.6 - - - +
1429B THR 3.0 0.2 - - - -
1430B LEU* 1.3 81.0 - - - +
1432B SER* 1.3 62.6 + - - +
1433B ARG 5.1 0.9 - - - -
1434B PRO* 5.5 0.3 - - - +
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Residues in contact with SER1432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1428B GLN 3.0 17.9 + - - -
1429B THR* 3.8 5.2 - - - +
1431B GLU* 1.3 84.3 - - - +
1433B ARG* 1.3 62.0 + - - +
1434B PRO* 2.9 15.3 - - - +
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Residues in contact with ARG1433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1326B ASP 4.7 1.7 - - - +
1371B GLY* 5.8 4.9 - - - -
1375B VAL 5.1 3.6 + - - -
1376B PRO* 3.4 47.7 - - + +
1377B ALA* 4.9 5.1 + - - +
1401B LYS 4.2 6.5 + - - -
1402B ALA* 3.4 32.9 - - - +
1403B GLY 5.2 0.6 - - - +
1429B THR* 2.9 30.9 + - - +
1430B LEU* 4.3 7.7 - - - +
1431B GLU 5.1 1.1 - - - -
1432B SER* 1.3 81.1 + - - +
1434B PRO* 1.4 65.0 - - + +
1435B SER 4.2 0.2 + - - -
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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