Contacts of the helix formed by residues 1388 - 1399 (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 THR1388 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1351B GLU* 2.6 34.7 + - + +
1385B PRO 5.3 3.1 - - - +
1386B THR* 2.7 23.2 + - - +
1387B ASP* 1.3 80.8 - - - +
1389B GLU* 1.3 69.8 + - - +
1390B ALA 4.4 0.4 - - - -
1391B GLU* 3.6 11.5 + - - +
1392B LEU* 3.3 13.9 + - - +
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Residues in contact with GLU1389 (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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1387B ASP 4.7 1.0 - - - +
1388B THR* 1.3 73.4 - - - +
1390B ALA* 1.3 65.4 + - - +
1392B LEU* 3.0 20.0 + - - +
1393B ASN* 2.6 44.6 + - - +
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Residues in contact with ALA1390 (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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1351B GLU* 3.0 34.1 - - - +
1353B LEU* 3.9 18.1 - - + +
1388B THR* 4.0 0.4 + - - -
1389B GLU* 1.3 80.3 - - - +
1391B GLU* 1.3 67.9 + - - +
1393B ASN* 3.0 22.1 + - - +
1394B LEU 3.5 3.8 + - - -
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Residues in contact with GLU1391 (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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1334B VAL* 3.9 19.9 - - + +
1335B ARG* 6.0 0.2 - - - +
1338B LYS* 2.8 31.5 + - - -
1349B ALA 5.7 0.2 - - - +
1351B GLU* 3.0 29.9 - - + -
1352B ASN 2.8 27.9 + - - +
1353B LEU* 4.3 7.4 - - - +
1356B LEU* 4.1 9.4 - - + +
1386B THR* 3.3 22.5 + - - +
1387B ASP* 3.8 9.1 - - - +
1388B THR* 3.6 7.8 + - - +
1389B GLU 3.1 0.6 + - - -
1390B ALA* 1.3 79.3 - - - +
1392B LEU* 1.3 66.5 + - - +
1394B LEU* 3.1 13.3 + - - +
1395B LEU* 3.4 7.4 + - - +
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Residues in contact with LEU1392 (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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1334B VAL* 3.5 29.4 - - + -
1381B ILE* 4.5 12.3 - - + -
1383B ALA* 5.7 4.7 - - - -
1387B ASP* 3.3 25.4 - - + +
1388B THR 3.3 13.0 - - - +
1389B GLU* 3.0 18.5 + - - +
1391B GLU* 1.3 76.9 - - - +
1393B ASN* 1.3 66.2 + - - +
1395B LEU* 2.9 13.4 + - + +
1396B TYR* 2.8 47.1 + - + +
1406B VAL* 5.8 7.0 - - + -
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Residues in contact with ASN1393 (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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1389B GLU* 2.6 49.7 + - - +
1390B ALA* 3.0 14.0 - - - +
1392B LEU* 1.3 73.8 - - - +
1394B LEU* 1.3 63.2 + - - +
1396B TYR* 3.1 33.3 - - - +
1397B GLU* 3.4 14.7 - - - +
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Residues in contact with LEU1394 (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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1353B LEU* 3.1 48.7 - - + +
1356B LEU* 3.8 15.0 - - + -
1357B ARG* 3.6 31.4 - - + +
1390B ALA 3.5 5.6 + - - +
1391B GLU 3.1 10.4 + - - +
1393B ASN* 1.3 75.4 - - - +
1395B LEU* 1.3 68.3 + - - +
1397B GLU* 2.9 23.3 - - - +
1398B LEU* 2.7 46.0 - - + +
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Residues in contact with LEU1395 (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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1332B ALA* 6.1 0.2 - - + -
1333B THR 4.6 3.1 - - - +
1334B VAL* 4.3 22.2 - - + -
1337B LEU* 4.0 26.2 - - + -
1356B LEU* 3.8 19.2 - - + +
1360B PHE* 4.0 18.2 - - + -
1363B LEU* 4.4 7.9 - - + -
1381B ILE* 3.6 43.5 - - + -
1391B GLU 3.4 2.7 + - - +
1392B LEU* 2.9 13.4 + - + +
1394B LEU* 1.3 79.8 - - - +
1396B TYR* 1.3 71.2 + - + +
1397B GLU 3.0 0.3 + - - -
1398B LEU* 3.2 12.9 + - - +
1399B CYS* 3.2 16.9 - - - -
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Residues in contact with TYR1396 (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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1381B ILE* 6.0 7.2 - - + -
1392B LEU* 2.8 43.5 + - + +
1393B ASN* 3.1 25.1 - - - +
1395B LEU* 1.3 80.1 - - + +
1397B GLU* 1.3 63.1 + - - +
1399B CYS* 3.5 16.0 - - - +
1404B ALA* 4.7 7.0 - - - +
1405B GLU 6.3 0.9 - - - -
1406B VAL* 4.4 28.0 - - + +
1421B GLU* 5.6 0.2 + - - -
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Residues in contact with GLU1397 (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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1393B ASN* 3.4 15.4 - - - +
1394B LEU* 2.9 33.9 - - - +
1396B TYR* 1.3 73.1 - - - +
1398B LEU* 1.3 57.9 + - + +
1399B CYS 2.5 21.2 + - - -
1400B ALA* 2.9 17.9 + - - +
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Residues in contact with LEU1398 (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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1356B LEU* 5.6 0.9 - - + +
1357B ARG* 4.3 28.0 - - + +
1360B PHE* 3.5 47.3 - - + -
1364B GLU* 5.0 3.2 - - - +
1394B LEU* 2.7 54.1 - - + +
1395B LEU* 3.2 9.1 + - - +
1397B GLU* 1.3 80.7 - - + +
1399B CYS* 1.3 50.6 + - - +
1400B ALA* 2.5 20.8 + - - +
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Residues in contact with CYS1399 (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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1360B PHE* 4.1 19.5 - - - -
1363B LEU* 4.7 2.2 - - - -
1379B VAL* 3.9 30.5 - - + -
1395B LEU* 3.2 24.2 - - - -
1396B TYR* 3.5 9.6 - - - +
1397B GLU 2.5 7.2 + - - -
1398B LEU* 1.3 68.7 - - - +
1400B ALA* 1.3 51.8 + - - +
1401B LYS* 2.7 19.8 + - - +
1402B ALA 3.5 14.4 + - - +
1404B ALA* 3.7 24.4 - - + +
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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