Contacts of the helix formed by residues 1538 - 1543 (chain E) 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 ARG1538 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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856E PHE* 5.8 5.1 + - - +
861E ILE* 5.3 8.5 - - - +
888E HIS* 3.6 17.6 + - - +
889E LYS* 3.2 59.0 - - - +
891E GLN* 5.4 5.1 - - - +
1508E THR* 4.8 16.3 + - - +
1509E ALA* 5.0 8.0 + - - +
1511E ILE 5.2 4.8 + - - -
1513E MET* 5.0 6.6 - - - +
1516E GLU* 3.1 37.8 + - - +
1536E ALA* 3.3 18.7 - - + +
1537E HIS* 1.3 87.7 + - + +
1539E VAL* 1.3 65.7 + - - +
1540E HIS* 3.1 5.8 - - + +
1541E THR* 3.0 12.9 + - - +
1542E ILE 3.6 0.2 + - - -
1580E ASP* 5.9 1.9 + - - -
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Residues in contact with VAL1539 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861E ILE* 6.2 4.0 - - + -
1377E CYS* 4.8 11.7 - - + -
1378E GLY 6.1 0.2 - - - +
1536E ALA* 5.0 2.9 - - - +
1537E HIS 4.1 1.1 - - - -
1538E ARG* 1.3 67.2 - - - +
1540E HIS* 1.3 60.2 + - + +
1541E THR 2.9 4.9 - - - -
1542E ILE* 2.6 29.9 + - + +
1543E LEU* 3.0 15.8 + - - +
1573E PHE* 3.5 31.4 - - + -
1576E PHE* 4.1 13.0 - - + +
1577E VAL* 4.1 27.8 - - + -
1580E ASP* 3.4 27.1 + - + +
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Residues in contact with HIS1540 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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928E LYS 4.2 18.2 + - - -
929E THR* 4.3 23.0 + - - -
1516E GLU* 5.2 5.6 + - - +
1517E ASN* 3.6 28.7 + - - -
1538E ARG* 3.1 7.8 - - + -
1539E VAL* 1.3 81.3 - - + +
1541E THR* 1.3 58.2 + - - +
1543E LEU* 4.1 20.6 + - + +
1544E SER* 5.3 0.7 + - - -
1577E VAL* 6.1 0.2 - - - -
1580E ASP* 6.4 1.6 - - + -
1581E LYS 6.3 2.5 - - - -
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Residues in contact with THR1541 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1508E THR* 4.9 8.4 - - - -
1516E GLU* 2.4 38.2 + - + +
1520E GLN* 3.2 43.8 + - + +
1524E MET* 5.5 1.0 - - - +
1534E THR* 6.3 1.8 - - - -
1536E ALA* 4.5 9.2 - - + -
1538E ARG* 3.0 12.1 + - - +
1539E VAL 2.9 0.4 - - - -
1540E HIS* 1.3 78.1 + - - +
1542E ILE* 1.3 58.4 + - - +
1543E LEU 3.2 2.6 + - - -
1544E SER* 3.2 22.7 + - - -
1545E ALA* 4.7 0.3 + - - +
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Residues in contact with ILE1542 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1375E GLY* 3.5 42.0 - - - -
1376E ILE 3.6 6.7 - - - +
1377E CYS* 3.7 27.4 - - + -
1534E THR* 4.6 6.3 - - - +
1536E ALA* 4.4 9.4 - - + +
1538E ARG 3.6 0.6 + - - -
1539E VAL* 2.6 31.0 + - + +
1541E THR* 1.3 70.2 - - - +
1543E LEU* 1.3 56.2 + - - +
1544E SER 2.9 11.8 + - - -
1545E ALA* 3.3 14.0 + - + +
1548E VAL* 4.0 21.4 - - + +
1562E PRO* 4.3 0.2 - - - +
1573E PHE* 3.4 31.4 - - + -
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Residues in contact with LEU1543 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1539E VAL 3.0 34.7 + - - +
1540E HIS* 4.1 16.2 - - + +
1541E THR 3.2 1.8 - - - -
1542E ILE* 1.3 76.1 - - - +
1544E SER* 1.3 58.7 + - - +
1562E PRO* 4.2 21.0 - - + +
1566E LEU* 3.8 29.2 - - + -
1573E PHE* 3.7 23.8 - - + -
1577E VAL* 4.0 21.1 - - + -
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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