Contacts of the helix formed by residues 1506 - 1511 (chain G) in PDB entry 6C3P
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 GLU1506 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1426G GLN* 3.1 33.2 + - - +
1505G ASP* 1.3 65.8 - - - +
1507G ALA* 1.3 64.8 + - - +
1508G THR 3.0 4.4 + - - -
1509G ALA* 3.1 10.2 + - - +
1535G ILE* 3.1 38.7 + - + +
1536G ALA* 4.2 0.4 - - - +
1537G HIS* 3.5 33.7 - - + +
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Residues in contact with ALA1507 (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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1424G ILE* 3.6 19.1 - - + -
1425G LEU 4.9 0.2 - - - -
1426G GLN 5.2 1.1 - - - -
1487G GLN* 3.3 18.6 + - - +
1491G LEU* 3.6 31.6 - - + -
1504G MET* 4.4 15.8 - - + +
1505G ASP 3.1 5.8 + - - +
1506G GLU* 1.3 76.2 - - - +
1508G THR* 1.3 57.9 + - - +
1509G ALA* 3.2 1.5 + - - +
1510G SER 4.0 2.1 + - - -
1511G ILE* 3.1 19.4 - - - +
1535G ILE 4.2 2.2 + - - -
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Residues in contact with THR1508 (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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1491G LEU* 6.3 0.4 - - - -
1506G GLU 3.0 1.6 + - - -
1507G ALA* 1.3 74.0 - - - +
1509G ALA* 1.3 64.0 + - - +
1510G SER 3.2 2.7 - - - -
1511G ILE* 2.9 35.1 + - - +
1516G GLU* 4.2 28.4 - - - +
1519G LEU* 6.5 1.3 - - - -
1536G ALA* 6.4 1.8 - - - -
1537G HIS 6.3 0.9 - - - -
1538G ARG* 4.8 10.8 + - - +
1541G THR* 4.9 9.4 - - - -
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Residues in contact with ALA1509 (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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857G SER* 3.6 33.5 + - - +
858G ALA 5.8 0.2 - - - +
888G HIS* 4.4 10.0 - - - +
1426G GLN* 3.6 17.0 - - - +
1506G GLU 3.1 16.7 + - - +
1507G ALA 3.2 0.4 - - - -
1508G THR* 1.3 78.9 - - - +
1510G SER* 1.3 61.6 + - - +
1511G ILE 3.4 3.5 + - - +
1537G HIS* 4.1 21.1 - - + +
1538G ARG* 5.0 11.5 + - - +
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Residues in contact with SER1510 (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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715G VAL* 5.0 1.0 - - - +
857G SER* 3.6 15.4 + - - -
888G HIS* 3.0 28.7 + - - -
1426G GLN 5.1 1.9 + - - -
1428G PRO* 4.9 6.6 - - - +
1483G GLN* 4.6 10.6 + - - +
1484G GLY* 4.2 19.7 + - - -
1487G GLN* 4.2 32.1 + - - +
1507G ALA 4.0 1.8 + - - -
1508G THR 3.2 0.8 - - - -
1509G ALA* 1.3 77.7 - - - +
1511G ILE* 1.3 58.6 + - - +
1512G ASP 3.8 0.3 + - - -
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Residues in contact with ILE1511 (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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715G VAL* 5.4 5.2 - - + -
888G HIS* 4.1 7.2 - - - +
1484G GLY* 4.9 1.8 - - - +
1487G GLN* 3.6 20.0 - - + -
1488G LEU* 3.5 28.5 - - + -
1491G LEU* 4.9 8.5 - - + -
1507G ALA 3.1 28.5 - - - +
1508G THR* 2.9 24.3 + - - +
1509G ALA 4.0 3.5 - - - +
1510G SER* 1.3 80.4 - - - +
1512G ASP* 1.3 82.3 + - - +
1515G THR* 3.8 10.1 - - + +
1516G GLU* 3.3 29.7 - - + +
1519G LEU* 5.2 5.2 - - + -
1538G ARG* 5.2 3.3 + - - -
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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