Contacts of the helix formed by residues 1340 - 1359 (chain N) in PDB entry 5D4D
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 GLY1340 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1335N LEU 3.4 1.0 + - - +
1336N LEU* 3.0 24.5 + - - -
1338N ALA 3.5 1.6 + - - -
1339N LYS* 1.3 78.6 - - - +
1341N PRO* 1.3 75.7 - - - +
1342N GLU* 3.5 2.7 - - - -
1343N ALA* 3.2 12.8 + - - +
1344N VAL* 3.2 14.7 + - - +
1419N PRO* 5.7 0.7 - - - -
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Residues in contact with PRO1341 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1336N LEU* 3.5 12.8 - - + -
1340N GLY* 1.3 80.3 - - - +
1342N GLU* 1.3 80.2 + - + +
1344N VAL* 3.0 4.5 + - + +
1345N GLU* 2.9 33.6 + - - +
1376N MET* 3.8 15.7 - - + -
1419N PRO* 3.8 29.8 - - + -
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Residues in contact with GLU1342 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1339N LYS 5.4 0.7 - - - +
1340N GLY 3.5 1.1 - - - -
1341N PRO* 1.3 90.2 - - - +
1343N ALA* 1.3 57.5 + - - +
1345N GLU* 3.4 14.7 + - - +
1346N ARG* 3.0 43.4 + - - +
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Residues in contact with ALA1343 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1335N LEU* 4.1 10.4 - - + +
1339N LYS* 3.6 46.1 + - + +
1340N GLY 3.2 11.3 + - - +
1341N PRO 3.1 0.4 - - - -
1342N GLU* 1.3 80.2 - - - +
1344N VAL* 1.3 56.4 + - - +
1346N ARG* 3.3 16.0 + - - +
1347N TYR* 2.9 30.3 + - - +
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Residues in contact with VAL1344 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1332N PRO* 4.0 13.0 - - + +
1335N LEU* 4.3 11.4 - - + -
1336N LEU* 3.4 40.8 - - + +
1340N GLY 3.2 17.3 - - - +
1341N PRO* 3.0 5.6 + - + +
1343N ALA* 1.3 75.3 - - - +
1345N GLU* 1.3 58.4 + - - +
1347N TYR* 3.7 1.6 - - + +
1348N LEU* 2.9 40.2 + - + +
1376N MET* 4.6 10.1 - - - -
1421N LEU* 3.8 28.9 - - + -
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Residues in contact with GLU1345 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1192N LEU* 3.5 54.7 - - + +
1341N PRO* 2.9 24.8 + - - +
1342N GLU* 3.7 16.1 - - - +
1344N VAL* 1.3 73.6 - - - +
1346N ARG* 1.3 64.7 + - - +
1349N VAL* 2.9 31.1 + - - +
1372N VAL* 3.9 18.2 - - + -
1373N ARG* 5.3 1.6 - - - -
1376N MET* 3.4 30.9 - - + +
1397N LYS* 5.6 1.9 + - - -
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Residues in contact with ARG1346 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1119N SER 5.3 6.5 + - - -
1121N PRO* 5.4 16.4 - - + -
1192N LEU* 5.5 1.7 - - - +
1339N LYS* 4.7 13.7 - - - +
1342N GLU* 3.0 27.0 + - - +
1343N ALA* 3.6 22.7 + - - +
1345N GLU* 1.3 75.4 - - - +
1347N TYR* 1.3 57.1 - - - +
1349N VAL* 4.0 4.5 - - - +
1350N GLU* 3.0 33.9 + - + +
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Residues in contact with TYR1347 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1258N ARG* 3.5 19.2 + - - -
1262N LEU* 4.6 7.0 - - + -
1328N GLY 5.0 0.2 + - - -
1329N ALA* 3.8 2.8 - - - -
1330N ILE* 3.0 65.9 + - + +
1332N PRO* 4.8 8.1 - - + -
1335N LEU* 3.7 20.4 - - + -
1343N ALA 2.9 17.3 + - - +
1344N VAL* 3.7 3.4 - - - +
1346N ARG* 1.3 74.5 - - - +
1348N LEU* 1.3 76.9 + - + +
1350N GLU* 3.3 3.0 + - + +
1351N GLU* 2.9 60.9 + - + +
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Residues in contact with LEU1348 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1262N LEU* 3.8 39.0 - - + +
1265N ALA* 5.6 0.2 - - - -
1332N PRO* 4.3 17.7 - - + -
1344N VAL* 2.9 32.7 + - + +
1345N GLU 4.0 2.2 - - - +
1347N TYR* 1.3 75.2 - - + +
1349N VAL* 1.3 64.6 + - - +
1351N GLU* 4.0 1.7 - - - +
1352N ILE* 2.9 34.9 + - + +
1372N VAL* 4.0 20.0 - - + -
1375N MET* 3.8 31.6 - - + -
1376N MET* 5.7 0.2 - - - -
1421N LEU* 4.1 17.9 - - + -
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Residues in contact with VAL1349 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1192N LEU* 4.9 4.3 - - + -
1345N GLU 2.9 22.9 + - - +
1346N ARG* 4.0 4.3 - - - +
1348N LEU* 1.3 76.6 - - - +
1350N GLU* 1.3 65.2 + - - +
1352N ILE* 3.8 1.9 - - - +
1353N GLN* 2.9 27.5 + - + +
1365N ASP* 4.3 29.4 - - + +
1368N ILE* 4.1 20.8 - - + +
1369N GLU* 3.8 33.0 - - + +
1372N VAL* 4.1 13.2 - - + -
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Residues in contact with GLU1350 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124N GLN* 4.3 14.2 + - - -
1135N ARG* 3.4 15.1 + - - -
1139N ASP* 5.1 0.2 - - - +
1346N ARG* 3.0 20.7 + - + +
1347N TYR* 4.1 3.1 - - + +
1349N VAL* 1.3 79.5 - - - +
1351N GLU* 1.3 61.1 + - + +
1353N GLN* 3.3 3.8 + - - +
1354N LYS* 2.9 44.1 + - - +
1357N ARG* 2.6 47.3 + - - -
1365N ASP* 5.6 0.7 - - - +
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Residues in contact with GLU1351 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1258N ARG* 3.1 22.8 + - - +
1262N LEU* 3.6 22.2 - - + +
1347N TYR* 2.9 55.7 + - + +
1348N LEU 4.0 0.9 - - - +
1350N GLU* 1.3 76.6 - - + +
1352N ILE* 1.3 66.6 + - - +
1354N LYS* 3.0 56.7 + - - +
1355N VAL* 3.8 9.7 + - - +
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Residues in contact with ILE1352 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1229N ILE* 5.5 0.2 - - + -
1259N VAL* 4.6 5.4 - - + +
1262N LEU* 3.4 30.9 - - + +
1263N PHE* 3.6 44.2 - - + +
1348N LEU* 2.9 30.7 + - + +
1349N VAL 3.8 2.9 - - - +
1351N GLU* 1.3 75.0 - - - +
1353N GLN* 1.3 63.4 + - - +
1354N LYS 3.3 0.7 + - - -
1355N VAL* 3.4 10.3 + - - +
1356N TYR* 3.3 33.1 - - + -
1368N ILE* 3.6 31.0 - - + -
1372N VAL* 4.7 2.9 - - + -
1375N MET* 5.9 0.2 - - - -
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Residues in contact with GLN1353 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1142N ALA* 4.7 2.8 - - - +
1349N VAL* 2.9 22.3 + - + +
1350N GLU* 3.6 6.3 - - - +
1352N ILE* 1.3 75.0 - - - +
1354N LYS* 1.3 65.2 + - - +
1356N TYR* 3.2 13.8 + - - +
1357N ARG* 2.9 54.8 + - - +
1361N VAL 5.1 0.7 - - - +
1363N LEU* 2.7 32.6 + - - +
1365N ASP* 2.5 40.0 + - - +
1368N ILE* 3.5 20.7 - - + +
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Residues in contact with LYS1354 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1350N GLU* 2.9 28.3 + - + +
1351N GLU* 3.0 44.9 + - - +
1353N GLN* 1.3 77.7 - - - +
1355N VAL* 1.3 58.4 + - + +
1357N ARG* 3.3 20.1 + - - +
1358N ALA* 2.9 30.6 + - - +
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Residues in contact with VAL1355 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1236N LEU* 4.3 10.8 - - + -
1254N GLN* 5.4 1.8 - - - -
1255N GLY* 3.7 37.9 - - - +
1258N ARG* 3.9 24.2 - - + -
1259N VAL* 3.7 24.9 - - + -
1351N GLU 3.8 13.2 - - - +
1352N ILE* 3.7 7.6 - - - +
1353N GLN 3.2 0.4 - - - -
1354N LYS* 1.3 76.0 - - + +
1356N TYR* 1.3 61.6 + - - +
1358N ALA* 3.1 18.0 + - + +
1359N GLN* 3.2 16.1 + - + +
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Residues in contact with TYR1356 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094N LEU* 4.9 4.0 - - - +
1229N ILE* 2.9 43.7 + - + +
1232N PRO* 3.7 12.8 - - + -
1233N GLY* 5.4 1.6 - - - -
1236N LEU* 3.9 26.7 - - + +
1259N VAL* 3.9 24.0 - - + +
1352N ILE* 3.3 35.7 - - + -
1353N GLN* 3.2 15.7 + - - +
1355N VAL* 1.3 77.7 - - + +
1357N ARG* 1.3 64.7 + - - +
1359N GLN 3.2 5.4 + - - +
1361N VAL* 2.8 56.7 + - + +
1363N LEU* 3.8 22.2 - - + -
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Residues in contact with ARG1357 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1135N ARG* 3.1 15.4 - - - +
1139N ASP* 3.0 42.4 + - - +
1142N ALA* 6.0 2.4 - - - +
1350N GLU* 2.6 52.3 + - - -
1353N GLN* 2.9 40.3 + - - +
1354N LYS* 3.5 17.8 - - - +
1356N TYR* 1.3 76.0 - - - +
1358N ALA* 1.3 59.6 + - - +
1360N GLY* 3.0 19.6 + - - -
1361N VAL 4.3 6.0 + - - +
1365N ASP* 4.8 6.3 + - - -
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Residues in contact with ALA1358 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1354N LYS 2.9 12.6 + - - +
1355N VAL* 3.1 14.1 + - + +
1357N ARG* 1.3 77.1 - - - +
1359N GLN* 1.3 71.1 + - - +
1360N GLY 3.3 0.6 + - - -
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Residues in contact with GLN1359 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1235N GLN* 3.8 16.1 - - + +
1236N LEU* 3.5 34.5 - - + -
1237N THR* 3.4 39.2 + - - +
1254N GLN* 5.9 1.4 + - - +
1255N GLY* 5.3 2.8 - - - +
1355N VAL* 3.2 11.0 + - + +
1356N TYR 3.2 3.5 + - - +
1357N ARG 3.2 0.8 - - - -
1358N ALA* 1.3 87.7 + - - +
1360N GLY* 1.3 61.7 + - - +
1361N VAL* 3.4 9.8 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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