Contacts of the helix formed by residues 1534 - 1542 (chain D) in PDB entry 5Z58
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 HIS1534 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1532D ILE* 3.5 1.9 - - + +
1533D SER* 1.3 75.9 - - - +
1535D THR* 1.3 60.3 + - - +
1536D GLN* 3.4 2.0 - - + -
1537D THR* 3.1 16.0 + - - +
1538D ARG* 3.0 25.2 + - - +
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Residues in contact with THR1535 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1533D SER 3.1 8.4 + - - -
1534D HIS* 1.3 68.5 - - - +
1536D GLN* 1.3 67.1 + - - +
1538D ARG* 3.7 6.6 - - - +
1539D LEU* 2.9 28.1 + - - +
1667D GLN* 6.4 1.6 - - - -
1676D TYR* 5.7 9.6 - - - -
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Residues in contact with GLN1536 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604D THR* 5.5 9.6 - - - -
1534D HIS* 3.4 0.8 - - + -
1535D THR* 1.3 78.2 - - - +
1537D THR* 1.3 65.7 + - - +
1539D LEU* 3.1 4.0 + - - +
1540D LEU* 2.9 25.8 + - - +
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Residues in contact with THR1537 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600D GLY* 4.8 15.3 - - - -
603D ARG* 6.1 2.6 - - - +
604D THR* 5.5 12.7 - - - +
1532D ILE* 4.8 9.4 - - - -
1534D HIS* 3.1 18.7 + - - +
1536D GLN* 1.3 78.8 - - - +
1538D ARG* 1.3 56.9 + - - +
1540D LEU* 3.3 7.1 + - - +
1541D SER* 2.9 32.4 + - - -
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Residues in contact with ARG1538 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1530D PHE* 5.3 12.7 - - + +
1532D ILE* 3.4 35.1 - - + +
1534D HIS 3.0 11.2 + - - +
1535D THR* 3.7 8.7 - - - +
1537D THR* 1.3 75.8 - - - +
1539D LEU* 1.3 64.5 + - - +
1541D SER* 3.0 14.9 + - - -
1542D MET* 3.0 15.5 + - - +
1707D GLN* 6.4 0.9 - - + -
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Residues in contact with LEU1539 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1535D THR 2.9 19.3 + - - +
1536D GLN* 3.6 4.7 - - - +
1538D ARG* 1.3 77.8 - - - +
1540D LEU* 1.3 61.8 + - - +
1542D MET* 3.5 11.7 + - - +
1543D ALA* 3.8 7.4 + - - +
1665D ASP* 4.9 19.2 - - + +
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Residues in contact with LEU1540 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603D ARG* 4.9 19.1 - - + +
604D THR* 6.3 0.4 - - - -
1536D GLN 2.9 16.9 + - - +
1537D THR* 3.6 7.9 - - - +
1539D LEU* 1.3 78.0 - - - +
1541D SER* 1.3 58.8 + - - +
1542D MET 3.1 0.4 - - - -
1543D ALA* 3.1 28.2 + - - +
1544D LYS 4.8 0.2 + - - -
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Residues in contact with SER1541 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603D ARG* 6.3 3.1 - - - -
1537D THR 2.9 17.1 + - - -
1538D ARG* 3.0 5.3 + - - -
1540D LEU* 1.3 76.9 - - - +
1542D MET* 1.3 59.0 + - - +
1543D ALA 3.3 0.6 + - - -
1544D LYS* 4.8 4.5 + - - +
1545D PRO* 5.0 4.5 - - - +
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Residues in contact with MET1542 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1538D ARG 3.0 12.4 + - - +
1539D LEU* 3.5 8.2 + - - +
1540D LEU 3.1 0.8 - - - -
1541D SER* 1.3 79.3 - - - +
1543D ALA* 1.3 63.9 + - - +
1544D LYS 3.6 0.7 - - - -
1545D PRO* 3.6 12.8 - - + +
1546D VAL* 3.3 19.1 + - - +
1664D MET* 6.1 5.4 - - + -
1705D MET* 4.6 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