Contacts of the helix formed by residues 1381 - 1394 (chain B) in PDB entry 5TWV
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 THR1381 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1379B GLY 3.8 0.4 + - - -
1380B ARG* 1.3 78.3 - - - +
1382B GLY* 1.3 53.7 + - - +
1385B LYS* 2.6 34.4 + - - +
1537B ALA 5.2 2.3 - - - +
1538B HIS* 5.1 17.5 - - - -
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Residues in contact with GLY1382 (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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1380B ARG* 4.5 0.4 - - - +
1381B THR* 1.3 80.3 - - - +
1383B SER* 1.3 59.8 + - - +
1384B GLY 3.2 1.8 - - - -
1385B LYS* 3.7 8.7 - - - -
1386B SER* 2.6 34.7 + - - -
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Residues in contact with SER1383 (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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1361B VAL* 4.9 15.7 - - - +
1362B LEU* 4.4 4.8 - - - +
1380B ARG* 3.7 22.3 - - - +
1381B THR 3.6 1.2 - - - -
1382B GLY* 1.3 77.8 - - - +
1384B GLY* 1.3 50.4 + - - +
1386B SER* 4.8 0.2 - - - -
1387B SER* 2.6 33.0 + - - -
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Residues in contact with GLY1384 (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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1362B LEU* 4.9 4.0 - - - -
1377B ILE* 4.6 10.0 - - - +
1380B ARG* 4.7 6.1 + - - +
1381B THR 4.2 0.8 + - - -
1383B SER* 1.3 81.5 - - - +
1385B LYS* 1.3 54.6 + - - +
1387B SER* 3.5 11.9 - - - -
1388B PHE* 2.6 34.7 - - - +
1536B ILE* 5.6 0.2 - - - +
1552B LEU* 4.9 16.0 - - - +
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Residues in contact with LYS1385 (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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1377B ILE* 6.2 0.2 - - - -
1380B ARG 4.6 1.4 + - - -
1381B THR 2.6 29.1 + - - +
1382B GLY* 3.7 3.1 - - - -
1384B GLY* 1.3 76.4 - - - +
1386B SER* 1.3 57.3 + - - +
1388B PHE* 3.9 1.1 - - - +
1389B SER* 2.9 31.4 + - - -
1536B ILE* 4.1 28.7 - - + +
1537B ALA 5.9 1.1 - - - +
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Residues in contact with SER1386 (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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1354B TYR* 5.7 0.2 - - - -
1382B GLY* 2.6 26.3 + - - -
1383B SER 4.8 0.2 - - - -
1385B LYS* 1.3 77.1 - - - +
1387B SER* 1.3 58.9 + - - +
1389B SER* 4.1 4.2 - - - +
1390B LEU* 2.8 33.5 + - - +
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Residues in contact with SER1387 (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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1352B VAL* 5.7 3.4 - - - -
1354B TYR* 5.5 3.4 - - - -
1361B VAL* 5.1 7.9 - - - -
1362B LEU* 3.7 32.9 - - - +
1383B SER 2.6 27.4 + - - -
1384B GLY* 3.5 5.5 - - - -
1386B SER* 1.3 73.6 - - - +
1388B PHE* 1.3 60.4 + - - +
1390B LEU* 4.0 3.8 - - - +
1391B ALA* 2.9 31.7 + - - +
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Residues in contact with PHE1388 (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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1362B LEU* 5.3 1.5 - - - +
1377B ILE* 4.9 12.6 - - + -
1384B GLY* 2.6 24.8 + - - +
1385B LYS* 3.9 3.1 - - - +
1387B SER* 1.3 77.7 - - - +
1389B SER* 1.3 55.6 + - - +
1391B ALA* 3.8 4.1 - - - +
1392B PHE* 2.9 29.5 + - - +
1534B VAL* 6.1 4.9 - - + -
1536B ILE* 6.0 2.9 - - + -
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Residues in contact with SER1389 (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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1385B LYS 2.9 20.7 + - - -
1386B SER* 4.1 4.5 - - - -
1388B PHE* 1.3 75.0 - - - +
1390B LEU* 1.3 54.7 + - - +
1392B PHE* 3.1 6.3 + - - -
1393B PHE* 2.6 58.0 + - - -
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Residues in contact with LEU1390 (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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1354B TYR* 3.3 26.7 - - - +
1386B SER 2.8 24.9 + - - +
1387B SER* 4.0 3.4 - - - +
1389B SER* 1.3 72.9 - - - +
1391B ALA* 1.3 58.0 + - - +
1393B PHE* 4.5 3.1 - - - +
1394B ARG* 2.8 8.0 + - - -
1395B MET* 2.8 42.0 + - + -
1396B VAL* 4.2 2.8 + - + +
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Residues in contact with ALA1391 (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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1347B ILE* 5.9 5.2 - - + -
1362B LEU* 5.9 3.8 - - + -
1387B SER 2.9 20.3 + - - +
1388B PHE* 3.8 4.3 - - - +
1390B LEU* 1.3 76.2 - - - +
1392B PHE* 1.3 63.5 + - - +
1394B ARG* 3.2 13.4 + - - +
1396B VAL 5.3 5.2 - - - -
1403B ILE* 5.5 11.2 - - + -
1410B ILE* 5.4 6.2 - - - +
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Residues in contact with PHE1392 (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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1388B PHE 2.9 18.8 + - - +
1389B SER* 3.5 6.7 - - - +
1391B ALA* 1.3 77.0 - - - +
1393B PHE* 1.3 73.9 + + - +
1394B ARG* 3.4 2.1 + - - +
1418B LEU* 6.1 1.4 - - - +
1419B ARG* 5.9 1.6 - - - -
1422B LEU* 3.6 35.4 - - + +
1423B SER 4.2 13.2 - - - -
1424B ILE* 5.9 0.4 - - - -
1502B ILE* 3.9 39.3 - - + -
1503B PHE 5.0 1.8 - - - -
1504B ILE* 4.1 23.3 - - + -
1534B VAL* 5.9 4.9 - - + -
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Residues in contact with PHE1393 (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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509B LEU* 4.5 20.4 - - + -
510B LYS* 5.1 13.7 - - + -
1389B SER* 2.6 46.8 + - - +
1390B LEU* 4.2 5.2 - - - +
1392B PHE* 1.3 84.6 - + - +
1394B ARG* 1.3 67.6 + - - +
1395B MET* 4.5 6.2 - - + +
1415B LEU 5.5 0.5 - - - +
1419B ARG* 4.6 27.6 + - + +
1422B LEU* 5.7 7.9 - - + -
1423B SER 6.2 0.2 - - - -
1424B ILE* 3.6 31.4 - - + -
1504B ILE* 5.9 3.6 - - + -
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Residues in contact with ARG1394 (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 LEU 2.8 9.7 + - - -
1391B ALA 3.2 9.3 + - - +
1392B PHE 3.2 5.4 - - - +
1393B PHE* 1.3 80.5 - - - +
1395B MET* 1.3 61.7 + - - +
1396B VAL* 3.3 10.2 + - - +
1410B ILE* 5.3 16.6 - - + +
1415B LEU* 5.4 17.6 - - + +
1418B LEU* 5.7 7.9 - - + -
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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