Contacts of the helix formed by residues 1384 - 1393 (chain G) in PDB entry 6BAA
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 GLY1384 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1362G LEU* 3.7 8.5 - - - +
1380G ARG* 4.2 6.5 - - - +
1383G SER* 1.3 82.9 - - - +
1385G LYS* 1.3 59.4 + - - +
1386G SER 3.5 0.9 - - - -
1387G SER 3.6 0.8 + - - -
1388G PHE* 3.0 33.3 + - - +
1552G LEU* 4.0 18.3 - - - +
1555G GLY* 3.7 17.3 - - - -
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Residues in contact with LYS1385 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1377G ILE* 4.8 13.2 - - + +
1380G ARG* 5.1 4.8 - - - +
1381G THR 4.7 12.8 - - - +
1382G GLY 4.5 1.2 - - - -
1384G GLY* 1.3 76.1 - - - +
1386G SER* 1.3 57.4 + - - +
1388G PHE* 3.8 3.2 - - - +
1389G SER* 2.9 29.5 + - - -
1536G ILE* 4.6 19.9 - - + +
1537G ALA 4.8 6.7 - - - +
1552G LEU* 3.6 22.5 - - + +
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Residues in contact with SER1386 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1382G GLY* 3.7 22.2 + - - -
1384G GLY 3.5 0.2 - - - -
1385G LYS* 1.3 76.8 - - - +
1387G SER* 1.3 61.6 + - - +
1389G SER* 3.7 6.3 - - - -
1390G LEU* 2.8 30.0 + - - +
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Residues in contact with SER1387 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1352G VAL* 4.6 4.7 - - - +
1354G TYR* 5.6 5.8 - - - -
1361G VAL* 3.7 23.6 - - - -
1362G LEU* 3.7 29.2 - - - +
1382G GLY 4.2 3.7 + - - -
1383G SER* 4.0 10.3 - - - -
1384G GLY 3.6 1.8 + - - -
1385G LYS 3.4 0.6 - - - -
1386G SER* 1.3 74.6 - - - +
1388G PHE* 1.3 61.1 + - - +
1390G LEU* 3.4 6.7 + - - +
1391G ALA* 3.0 27.9 + - - +
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Residues in contact with PHE1388 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1362G LEU* 3.7 18.4 - - + +
1365G VAL* 5.7 6.5 - - + -
1384G GLY 3.0 20.1 + - - +
1385G LYS* 3.8 4.9 - - - +
1387G SER* 1.3 74.1 - - - +
1389G SER* 1.3 59.0 + - - +
1391G ALA* 3.3 4.5 + - - +
1392G PHE* 2.9 26.6 + - - +
1552G LEU* 6.1 3.1 - - + -
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Residues in contact with SER1389 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1385G LYS 2.9 20.2 + - - -
1386G SER* 3.7 7.2 - - - -
1387G SER 3.3 0.2 - - - -
1388G PHE* 1.3 75.2 - - - +
1390G LEU* 1.3 51.9 + - - +
1392G PHE* 2.9 9.3 + - - +
1393G PHE* 2.6 58.9 + - - -
1504G ILE* 5.9 2.2 - - - -
1536G ILE* 5.3 10.1 - - - -
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Residues in contact with LEU1390 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1354G TYR* 3.2 27.1 - - + +
1386G SER 2.8 22.2 + - - +
1387G SER* 3.6 7.4 - - - +
1389G SER* 1.3 72.4 - - - +
1391G ALA* 1.3 56.0 + - - +
1393G PHE* 3.4 6.2 - - - -
1394G ARG 2.8 7.1 + - - -
1395G MET* 2.5 42.2 + - + +
1396G VAL* 4.5 2.0 - - + +
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Residues in contact with ALA1391 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1350G LEU* 6.3 1.8 - - + -
1352G VAL* 5.6 5.8 - - + -
1362G LEU* 4.8 9.4 - - + -
1387G SER 3.0 14.6 + - - +
1388G PHE* 3.6 10.3 - - - +
1390G LEU* 1.3 72.3 - - - +
1392G PHE* 1.3 62.7 + - - +
1394G ARG* 3.0 17.2 + - - +
1396G VAL* 4.0 17.0 - - + +
1398G MET* 5.9 5.8 - - + +
1403G ILE* 4.9 19.9 - - + +
1410G ILE* 5.9 2.9 - - - +
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Residues in contact with PHE1392 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1388G PHE 2.9 14.6 + - - +
1389G SER* 3.2 12.3 - - - +
1391G ALA* 1.3 75.0 - - - +
1393G PHE* 1.3 66.9 + + - +
1394G ARG* 3.1 2.1 + - - +
1404G ILE 5.5 3.8 - - - -
1405G ILE* 4.6 21.1 - - + -
1410G ILE* 5.9 2.4 - - - +
1419G ARG* 5.9 0.9 - - - +
1422G LEU* 5.6 11.4 - - + -
1423G SER 6.0 0.9 - - - -
1424G ILE* 5.5 2.9 - - + -
1502G ILE* 3.8 29.4 - - + -
1503G PHE 4.6 5.8 - - - -
1504G ILE* 3.6 35.0 - - + -
1534G VAL* 5.4 9.0 - - + -
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Residues in contact with PHE1393 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511G LEU* 4.8 21.5 - - + -
1389G SER* 2.6 44.5 + - - +
1390G LEU* 3.8 8.5 - - - +
1392G PHE* 1.3 75.0 - + - +
1394G ARG* 1.3 67.9 + - - +
1395G MET* 4.5 4.7 - - + +
1419G ARG* 4.2 11.9 - - - +
1424G ILE* 3.6 25.1 - - + -
1504G ILE* 3.7 29.6 - - + -
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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