Contacts of the helix formed by residues 1320 - 1333 (chain I) in PDB entry 6ALH
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 PRO1320 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1291I LEU 4.5 0.2 - - - +
1292I THR* 3.6 24.0 - - + +
1296I ASP* 3.2 20.9 - - + +
1297I ASP* 4.7 2.0 - - + -
1319I MET* 1.3 95.5 - - + +
1321I GLU* 1.3 64.5 + - - +
1322I SER* 4.2 3.4 - - - +
1323I PHE* 3.3 22.0 + - + +
1324I ASN 3.7 1.7 + - - -
345J LYS* 3.5 19.1 - - - +
1352J ILE 4.1 7.4 - - - +
1353J VAL* 3.3 26.0 - - - +
1354J GLY* 3.9 6.7 - - - -
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Residues in contact with GLU1321 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1256I GLN* 4.3 11.7 - - + +
1296I ASP* 2.8 28.9 + - - +
1297I ASP* 5.1 5.3 - - - +
1298I VAL* 5.1 8.1 - - + +
1319I MET 3.5 4.4 + - - +
1320I PRO* 1.3 69.9 - - - +
1322I SER* 1.3 57.9 + - - +
1324I ASN* 2.9 37.4 + - - +
1325I VAL* 3.0 13.1 + - - +
96J LYS* 4.6 13.4 + - - -
99J ARG* 2.8 51.5 + - - +
100J GLU* 6.1 0.9 - - - +
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Residues in contact with SER1322 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1255I THR* 5.0 8.7 - - - -
1256I GLN 5.9 0.2 - - - +
1257I GLN* 3.6 22.9 - - - -
1296I ASP* 2.7 24.3 + - - -
1320I PRO* 4.2 0.3 - - - +
1321I GLU* 1.3 70.9 - - - +
1323I PHE* 1.3 61.6 + - - +
1325I VAL* 3.2 11.7 + - - +
1326I LEU* 2.9 28.4 + - - +
337J ARG* 6.0 0.2 - - - +
341J ASN* 3.6 7.7 + - - -
342J LEU* 3.9 15.3 - - - +
345J LYS* 3.6 18.9 + - - -
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Residues in contact with PHE1323 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1319I MET* 4.0 26.0 - - + -
1320I PRO* 3.3 15.5 + - + +
1322I SER* 1.3 82.5 + - - +
1324I ASN* 1.3 58.4 + - - +
1326I LEU* 3.3 11.8 + - + +
1327I LEU* 2.9 65.0 + - + +
1339I LEU* 4.3 13.2 - - + -
20J ILE* 3.8 29.4 - - + -
342J LEU* 4.7 4.5 - - + +
1320J ILE* 5.7 3.6 - - + -
1352J ILE* 3.6 44.2 - - + +
1353J VAL* 4.6 17.9 - - + -
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Residues in contact with ASN1324 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1319I MET* 4.8 13.8 - - - -
1320I PRO 3.7 3.9 + - - +
1321I GLU* 2.9 30.0 + - - +
1323I PHE* 1.3 80.6 - - - +
1325I VAL* 1.3 60.5 - - - +
1327I LEU* 3.3 11.1 + - - +
1328I LYS* 2.9 54.7 + - - +
99J ARG 5.9 0.8 + - - -
100J GLU* 5.0 16.4 + - - +
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Residues in contact with VAL1325 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1254I VAL 4.1 4.9 - - - +
1255I THR* 4.6 12.8 - - + -
1321I GLU* 3.0 15.0 + - + +
1322I SER* 3.2 13.4 + - - +
1324I ASN* 1.3 74.9 - - - +
1326I LEU* 1.3 59.4 + - - +
1328I LYS* 3.3 3.8 + - - +
1329I GLU* 2.9 33.0 + - + +
99J ARG* 3.8 30.3 - - + +
249J LEU* 3.7 34.5 - - + +
337J ARG* 4.7 19.5 - - - +
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Residues in contact with LEU1326 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1322I SER 2.9 13.6 + - - +
1323I PHE* 3.4 18.2 - - + +
1325I VAL* 1.3 76.9 - - - +
1327I LEU* 1.3 67.1 + - + +
1329I GLU* 3.2 7.7 + - - +
1330I ILE* 2.9 53.8 + - + +
331J ILE* 4.4 9.6 - - + -
337J ARG* 4.7 17.6 - - + +
338J PHE* 3.6 49.1 - - + -
342J LEU* 3.8 17.0 - - + -
1320J ILE* 6.3 0.7 - - + -
1352J ILE* 4.9 1.6 - - + -
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Residues in contact with LEU1327 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1323I PHE* 2.9 61.6 + - + +
1324I ASN* 3.7 13.9 - - - +
1325I VAL 3.3 0.2 - - - -
1326I LEU* 1.3 86.5 - - + +
1328I LYS* 1.3 60.1 + - + +
1330I ILE* 4.1 5.9 - - + +
1331I ARG* 2.9 48.6 + - - +
1337I ILE* 4.5 26.1 - - + +
1338I GLU 4.8 5.6 - - - +
1339I LEU* 4.5 20.4 - - + -
20J ILE* 5.9 0.9 - - + -
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Residues in contact with LYS1328 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1324I ASN* 2.9 50.6 + - - +
1325I VAL 3.3 4.0 + - - +
1327I LEU* 1.3 77.6 - - - +
1329I GLU* 1.3 57.1 + - - +
1331I ARG* 3.7 24.6 - - - +
1332I SER* 2.9 27.2 + - - -
99J ARG 4.4 11.0 - - - +
100J GLU* 3.2 34.9 - - - +
102J MET* 4.3 21.6 - - + +
245J LEU* 3.7 4.1 - - - +
246J PRO* 4.5 7.2 - - + +
249J LEU* 3.9 17.9 - - + -
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Residues in contact with GLU1329 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1325I VAL* 2.9 21.1 + - + +
1326I LEU* 3.7 9.4 - - + +
1328I LYS* 1.3 74.9 - - - +
1330I ILE* 1.3 61.4 + - - +
1332I SER* 2.3 30.7 + - - +
1333I LEU* 3.1 11.0 + - - +
245J LEU* 3.7 25.8 - - + +
249J LEU* 5.2 2.4 - - + +
265J LEU* 5.3 0.5 - - - +
327J LEU* 5.2 7.7 - - + +
330J MET* 3.3 42.8 - - - +
331J ILE* 3.9 17.6 - - + +
337J ARG* 3.7 29.4 + - - +
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Residues in contact with ILE1330 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1326I LEU* 2.9 43.0 + - + +
1327I LEU* 4.1 6.5 - - + +
1329I GLU* 1.3 75.7 - - - +
1331I ARG* 1.3 58.2 + - - +
1333I LEU* 3.1 26.7 + - + +
1335I ILE* 3.4 35.9 - - + +
1337I ILE* 4.0 22.7 - - + -
331J ILE* 4.1 19.3 - - + -
338J PHE* 5.0 5.6 - - + -
1332J LEU* 4.0 25.6 - - + -
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Residues in contact with ARG1331 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1327I LEU* 2.9 32.9 + - - +
1328I LYS* 4.0 27.2 - - - +
1330I ILE* 1.3 76.9 - - - +
1332I SER* 1.3 56.5 + - - +
1333I LEU 2.9 13.8 - - - +
1335I ILE 3.5 9.4 - - - +
1337I ILE* 2.5 33.7 + - + +
1338I GLU* 3.8 14.0 - - - +
1339I LEU* 5.2 0.4 - - - +
33J TRP* 3.5 55.4 - - + +
102J MET* 3.4 30.1 - - - +
243J PRO* 4.0 4.3 - - - +
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Residues in contact with SER1332 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1328I LYS 2.9 16.9 + - - -
1329I GLU* 2.3 29.2 + - - +
1331I ARG* 1.3 73.6 - - - +
1333I LEU* 1.3 62.3 + - - +
102J MET* 3.9 8.5 - - - -
242J LEU* 5.4 1.0 - - - +
243J PRO* 3.3 20.5 - - - +
245J LEU* 3.9 34.2 - - - +
269J TYR* 4.8 4.0 + - - -
306J LEU* 5.5 0.5 - - - +
307J LEU* 4.8 3.6 - - - +
327J LEU* 4.1 22.1 - - - +
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Residues in contact with LEU1333 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1329I GLU 3.1 8.8 + - - +
1330I ILE* 3.1 18.9 + - + +
1331I ARG 2.9 15.9 - - - +
1332I SER* 1.3 78.2 - - - +
1334I GLY* 1.3 61.4 + - - +
1335I ILE* 3.1 16.5 + - + -
25J ALA* 5.1 0.5 - - - +
33J TRP* 5.3 0.3 - - - -
113J HIS* 5.0 4.0 - - - +
115J TRP* 3.6 40.4 - - + -
243J PRO* 4.1 11.0 - - - +
307J LEU* 3.7 20.4 - - + +
327J LEU* 3.7 34.8 - - + -
331J ILE* 3.7 22.7 - - + -
1332J LEU* 5.5 0.4 - - + -
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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