Contacts of the helix formed by residues 1384 - 1394 (chain B) in PDB entry 4Z4Q
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 ILE1384 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1380B ARG* 3.4 20.2 - - + +
1381B VAL* 2.8 7.6 + - - +
1383B SER* 1.3 91.9 - - - +
1385B LEU* 1.3 64.0 + - - +
1386B ASP 3.1 3.3 + - - -
1387B GLU* 3.2 23.4 - - + +
1388B VAL* 3.0 36.1 + - + +
1409B TYR* 3.4 41.7 - - + -
1411B PHE* 4.3 12.3 - - + -
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Residues in contact with LEU1385 (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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1393A ARG* 3.8 39.3 - - - +
1424A LEU* 6.1 4.3 - - + -
1381B VAL* 2.8 25.5 + - + +
1382B ILE* 3.6 22.0 + - + +
1383B SER 3.6 2.4 - - - -
1384B ILE* 1.3 75.1 - - - +
1386B ASP* 1.3 60.6 + - - +
1388B VAL* 3.1 8.3 + - + +
1389B ILE* 2.9 47.8 + - + +
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Residues in contact with ASP1386 (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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1393A ARG* 2.4 42.3 + - - +
1384B ILE 3.2 0.8 - - - -
1385B LEU* 1.3 73.9 + - - +
1387B GLU* 1.3 75.8 + - - +
1389B ILE* 3.3 6.8 + - - +
1390B ALA* 2.9 25.6 + - - +
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Residues in contact with GLU1387 (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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1383B SER 4.7 1.8 - - - +
1384B ILE* 3.2 32.3 - - + +
1386B ASP* 1.3 81.0 + - - +
1388B VAL* 1.3 57.7 + - - +
1390B ALA* 3.4 7.5 + - - +
1391B LEU* 2.9 29.9 + - - +
1409B TYR* 3.4 27.3 + - + +
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Residues in contact with VAL1388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1424A LEU* 5.5 4.5 - - + -
1381B VAL* 4.7 21.8 - - + +
1384B ILE* 3.0 40.9 + - + +
1385B LEU* 3.5 12.6 - - + +
1387B GLU* 1.3 75.8 - - - +
1389B ILE* 1.3 61.8 + - + +
1391B LEU* 3.1 6.8 + - - +
1392B ILE* 2.8 48.0 + - + +
1405B LEU* 4.1 28.0 - - + -
1409B TYR* 4.9 3.8 - - + -
1411B PHE* 5.1 0.9 - - + -
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Residues in contact with ILE1389 (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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1389A ILE* 4.1 32.8 - - + -
1393A ARG* 4.7 20.6 - - - +
1424A LEU* 5.2 17.3 - - + -
1427A LEU* 4.5 13.0 - - + -
1385B LEU* 2.9 36.2 + - + +
1386B ASP* 3.8 7.2 - - - +
1388B VAL* 1.3 76.3 - - + +
1390B ALA* 1.3 66.6 + - - +
1392B ILE* 3.1 8.0 + - - +
1393B ARG* 2.8 31.5 + - + +
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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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1386B ASP 2.9 17.8 + - - +
1387B GLU* 3.5 8.5 - - - +
1389B ILE* 1.3 78.0 - - - +
1391B LEU* 1.3 58.4 + - - +
1393B ARG* 3.4 8.9 + - - +
1394B ALA* 3.0 27.5 + - - +
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Residues in contact with LEU1391 (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 GLU 2.9 15.8 + - - +
1388B VAL* 3.6 3.4 - - - +
1389B ILE 3.1 0.2 - - - -
1390B ALA* 1.3 75.8 - - - +
1392B ILE* 1.3 70.5 + - + +
1394B ALA* 3.1 15.3 + - + +
1395B SER* 2.8 20.9 + - - +
1401B ALA 4.2 4.7 - - - +
1404B ASN* 3.6 32.0 + - + +
1405B LEU* 4.2 19.3 - - + -
1408B SER* 3.8 19.5 - - - +
1409B TYR* 3.6 32.3 - - + -
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Residues in contact with ILE1392 (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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1424A LEU* 3.6 55.6 - - + +
1425A TYR* 4.4 3.1 - - - +
1427A LEU* 4.7 6.7 - - + -
1428A THR* 3.4 25.5 - - + +
1388B VAL* 2.8 35.4 + - + +
1389B ILE* 3.7 5.4 - - - +
1391B LEU* 1.3 81.1 - - + +
1393B ARG* 1.3 65.0 + - - +
1394B ALA 2.9 2.8 + - - -
1395B SER* 3.0 15.6 + - - -
1401B ALA* 4.5 12.8 - - + -
1405B LEU* 4.9 12.8 - - + -
1419B ILE 5.3 4.0 - - - +
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Residues in contact with ARG1393 (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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1385A LEU* 3.2 31.9 - - - +
1386A ASP* 3.3 35.6 + - - -
1389A ILE* 4.1 14.8 - - + -
1427A LEU* 3.9 26.2 + - + +
1428A THR 4.5 3.5 + - - +
1430A THR* 3.3 31.3 - - - +
1389B ILE* 2.8 24.5 + - + +
1390B ALA* 3.4 13.0 - - - +
1392B ILE* 1.3 72.6 - - - +
1394B ALA* 1.3 60.5 - - - +
1395B SER 3.5 5.7 + - - +
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Residues in contact with ALA1394 (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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1390B ALA 3.0 15.9 + - - +
1391B LEU* 3.4 11.2 - - - +
1392B ILE 2.9 1.6 - - - -
1393B ARG* 1.3 77.6 - - - +
1395B SER* 1.3 61.5 + - - +
1396B GLU* 5.5 1.4 - - - +
1400B ASP* 4.8 0.5 - - - +
1404B ASN* 5.4 1.7 + - - +
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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