Contacts of the helix formed by residues 1284 - 1292 (chain I) in PDB entry 6ALG
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 ALA1284 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1282I GLY 3.2 1.2 + - - -
1283I ALA* 1.3 73.9 - - - +
1285I TYR* 1.3 53.9 + - + +
1286I THR 3.2 1.3 - - - -
1287I LEU* 3.2 6.9 + - - +
1288I GLN* 2.6 34.7 + - - +
479J GLU* 2.7 11.7 + - - +
1356J LEU* 3.9 16.6 - - + +
1357J ILE* 4.3 20.9 + - + +
1360J GLY* 5.0 1.6 - - - -
1361J THR* 4.2 3.8 - - - +
1362J GLY* 3.7 28.7 - - - +
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Residues in contact with TYR1285 (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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1284I ALA* 1.3 70.1 - - + +
1286I THR* 1.3 58.3 + - - +
1288I GLN* 3.6 18.9 - - - +
1289I GLU* 2.9 31.4 + - - +
1315I MET* 4.8 7.6 - - - +
473J THR* 4.8 3.9 - - + +
475J GLU* 3.5 50.3 - - + -
476J ALA* 4.2 3.7 - - + +
479J GLU* 2.7 31.1 + - + +
1356J LEU* 4.1 28.1 - - + +
1361J THR* 3.6 28.4 + - + -
1362J GLY* 5.6 0.2 - - - -
1365J TYR* 5.1 7.1 - - - +
20K VAL* 5.4 0.2 - - + -
21K LEU* 3.4 21.8 - - + +
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Residues in contact with THR1286 (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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1278I LEU* 3.8 15.7 - - + -
1283I ALA* 4.2 6.7 - - - +
1285I TYR* 1.3 71.9 - - - +
1287I LEU* 1.3 58.2 + - - +
1289I GLU* 3.7 5.0 - - - +
1290I MET* 2.8 50.5 + - + +
422J LEU* 4.2 16.8 - - + -
471J PRO* 5.2 3.8 - - + -
476J ALA* 3.3 30.8 + - + +
479J GLU* 2.7 30.3 + - - +
480J ALA* 4.6 1.4 + - + -
484J MET* 5.0 2.7 - - - -
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Residues in contact with LEU1287 (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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1270I PHE* 5.4 0.7 - - + -
1275I VAL* 3.7 29.8 - - + +
1278I LEU* 3.7 32.8 - - + +
1279I GLU* 4.1 1.6 - - + +
1283I ALA 4.3 3.8 - - - +
1284I ALA* 3.2 9.5 + - - +
1286I THR* 1.3 78.4 - - - +
1288I GLN* 1.3 67.0 + - - +
1290I MET* 3.6 6.6 - - + +
1291I LEU* 3.0 56.7 + - + +
1351J VAL* 3.8 12.6 - - + -
1355J ARG 5.7 2.9 - - - +
1357J ILE* 3.7 33.7 - - + -
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Residues in contact with GLN1288 (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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1284I ALA 2.6 19.7 + - - +
1285I TYR* 3.2 17.7 + - - +
1287I LEU* 1.3 76.1 - - - +
1289I GLU* 1.3 58.4 + - - +
1291I LEU* 5.2 1.8 - - - -
1292I THR* 2.8 37.2 + - - +
1315I MET* 3.6 19.1 - - + +
1317I PRO* 3.3 30.3 - - - +
1354J GLY 4.0 19.3 + - - +
1355J ARG* 4.3 9.2 - - - +
1356J LEU* 3.3 35.3 - - + +
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Residues in contact with GLU1289 (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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1285I TYR 2.9 18.5 + - - +
1286I THR* 3.7 6.9 - - - +
1288I GLN* 1.3 77.8 - - - +
1290I MET* 1.3 61.8 + - - +
1291I LEU 3.2 0.2 - - - -
1292I THR 4.0 0.4 - - - -
1293I VAL* 4.0 17.7 - - + +
1294I LYS* 3.0 42.3 + - + +
1304I MET* 4.6 2.6 - - - +
1315I MET* 3.9 15.8 - - - +
470J VAL 4.1 1.6 - - - +
471J PRO* 3.4 5.5 - - - +
472J LEU* 2.8 35.0 + - - +
473J THR* 2.9 34.7 + - - +
476J ALA* 3.3 14.4 - - - +
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Residues in contact with MET1290 (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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1270I PHE* 3.6 38.3 - - + -
1278I LEU* 4.5 4.0 - - + -
1286I THR* 2.8 47.1 + - + +
1287I LEU* 3.6 10.8 - - + +
1288I GLN 3.1 0.6 - - - -
1289I GLU* 1.3 78.9 - - - +
1291I LEU* 1.3 62.0 + - + +
1294I LYS* 3.2 34.9 - - - +
1295I SER* 4.9 0.9 - - - -
347J VAL* 3.3 36.7 - - + +
422J LEU* 4.2 10.3 - - + -
469J HIS* 4.2 20.0 - - + -
470J VAL 5.0 2.7 - - - +
471J PRO* 5.8 0.2 - - + -
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Residues in contact with LEU1291 (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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1270I PHE* 6.0 1.6 - - + -
1275I VAL* 4.3 8.7 - - + -
1287I LEU* 3.0 42.8 + - + +
1288I GLN* 4.8 1.6 - - - +
1290I MET* 1.3 81.9 - - + +
1292I THR* 1.3 73.5 + - - +
1295I SER* 4.4 7.1 - - - +
1320I PRO* 4.0 0.2 - - - +
342J LEU 4.7 3.8 - - - +
343J LEU 4.3 13.0 - - - +
344J GLY* 5.9 0.2 - - - -
345J LYS* 2.4 58.5 + - + +
1351J VAL* 3.3 38.1 - - + +
1354J GLY* 4.3 9.0 - - - -
1355J ARG 5.9 0.9 - - - +
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Residues in contact with THR1292 (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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1288I GLN* 2.8 24.0 + - - -
1291I LEU* 1.3 82.4 + - - +
1293I VAL* 1.3 61.5 + - - +
1294I LYS 4.5 0.2 - - - +
1295I SER 2.9 16.3 - - - +
1297I ASP* 3.2 24.6 - - - +
1300I GLY* 5.2 0.2 - - - -
1317I PRO* 3.2 35.9 - - + +
1318I GLY 4.0 9.6 - - - +
1320I PRO* 4.3 14.3 - - + +
1354J GLY* 3.2 28.8 + - - +
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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
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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