Contacts of the helix formed by residues 1405 - 1412 (chain B) in PDB entry 2ZEJ
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 HIS1405 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1441A ARG* 3.5 24.5 - - - +
1402B TYR* 3.0 24.2 + + + +
1403B SER 3.4 1.0 - - - -
1404B THR* 1.3 78.8 - - - +
1406B PRO* 1.4 81.6 - - + +
1407B HIS* 3.1 37.3 + - + +
1408B PHE* 3.0 27.8 + + + -
1409B MSE 3.1 7.4 + - - -
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Residues in contact with PRO1406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1406A PRO* 4.1 28.7 - - + -
1409A MSE 5.7 1.6 - - + -
1410A THR* 3.7 29.4 - - + -
1441A ARG* 4.3 7.9 - - - +
1404B THR 3.2 5.8 - - - +
1405B HIS* 1.4 96.8 - - + +
1407B HIS* 1.3 63.1 + - - +
1409B MSE 4.1 8.7 - - + -
1410B THR* 2.9 31.3 + - + +
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Residues in contact with HIS1407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1405B HIS* 3.1 25.4 + - + +
1406B PRO* 1.3 76.1 - - - +
1408B PHE* 1.3 83.1 + + + +
1410B THR* 4.5 2.2 - - - -
1411B GLN* 2.8 61.9 + - + +
1412B ARG* 3.6 13.8 + - + +
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Residues in contact with PHE1408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1335A MSE 6.4 4.7 - - + -
1336A LYS* 3.8 13.1 - - - +
1402B TYR* 3.4 69.8 - + - -
1403B SER* 3.5 19.3 - - - +
1405B HIS* 3.0 16.3 + + + +
1407B HIS* 1.3 95.2 - + + +
1409B MSE 1.3 66.2 + - - +
1412B ARG* 3.3 44.2 + - + +
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Residues in contact with MSE1409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1336A LYS* 3.7 23.6 - - - +
1338A MSE 4.1 23.1 - - + +
1393A TRP* 3.7 44.0 - - + -
1395A PHE* 5.2 0.2 - - + -
1404A THR* 4.1 30.1 - - + +
1406A PRO* 5.9 0.9 - - + -
1409A MSE 5.3 8.7 - - + -
1404B THR* 3.3 34.8 - - - +
1405B HIS 3.1 7.0 + - - +
1406B PRO* 3.7 10.3 - - + +
1408B PHE* 1.3 79.5 - - - +
1410B THR* 1.3 66.1 + - + +
1413B ALA* 3.7 16.8 - - - +
1415B TYR* 4.5 1.7 + - - -
1441B ARG* 5.6 4.4 + - - +
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Residues in contact with THR1410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1406A PRO* 3.7 33.9 - - + -
1406B PRO* 2.9 25.2 + - + +
1407B HIS* 4.5 0.3 - - - -
1409B MSE 1.3 86.5 - - + +
1411B GLN* 1.3 72.4 + - - +
1412B ARG 3.6 0.4 - - - -
1413B ALA* 4.8 5.6 + - - +
1415B TYR* 5.0 1.5 + - - -
1441B ARG* 3.8 40.2 + - - +
1442B ALA* 3.3 19.4 - - - +
1445B SER* 4.4 3.6 + - - -
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Residues in contact with GLN1411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1407B HIS* 2.8 48.7 + - + +
1410B THR* 1.3 82.7 + - - +
1412B ARG* 1.3 64.6 + - + +
1413B ALA 3.6 1.6 - - - -
1441B ARG 3.4 21.7 - - - +
1442B ALA* 3.5 17.1 - - - +
1444B SER* 5.8 3.4 - - - -
1511B PHE* 3.4 16.7 - - - -
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Residues in contact with ARG1412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1335A MSE 4.2 25.3 + - + +
1336A LYS* 3.2 24.7 + - + +
1407B HIS* 4.4 14.8 - - - +
1408B PHE* 3.3 47.7 + - + +
1411B GLN* 1.3 86.5 + - - +
1413B ALA* 1.3 56.6 + - - +
1511B PHE* 3.5 39.3 + - + -
1512B LYS* 3.5 33.5 - - - +
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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