Contacts of the helix formed by residues 1414 - 1421 (chain D) in PDB entry 5TWV
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 PRO1414 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1412D LYS 4.1 3.8 - - - +
1413D LEU* 1.3 81.9 - - + +
1415D LEU* 1.3 56.0 + - - +
1416D HIS* 3.4 1.6 - - + +
1417D THR* 3.2 21.4 + - - +
1418D LEU* 2.7 35.0 + - - +
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Residues in contact with LEU1415 (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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1393D PHE 5.5 0.7 - - - +
1394D ARG* 5.4 16.2 - - + +
1413D LEU 3.2 7.2 + - - +
1414D PRO* 1.3 70.7 - - - +
1416D HIS* 1.3 59.1 + - - +
1418D LEU* 3.5 6.9 - - - +
1419D ARG* 2.9 32.3 + - - +
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Residues in contact with HIS1416 (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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511D LEU* 5.2 1.2 - - - +
1414D PRO* 4.9 0.8 - - + +
1415D LEU* 1.3 78.5 - - - +
1417D THR* 1.3 58.3 + - - +
1419D ARG* 4.3 3.5 - - - +
1420D SER* 2.9 32.2 + - - -
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Residues in contact with THR1417 (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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1414D PRO* 3.2 28.6 + - - +
1416D HIS* 1.3 77.4 - - - +
1418D LEU* 1.3 60.3 + - - +
1420D SER* 3.8 4.4 - - - -
1421D ARG* 2.9 32.3 + - - +
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Residues in contact with LEU1418 (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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1392D PHE 6.1 1.3 - - - +
1394D ARG* 5.7 8.1 - - + -
1413D LEU* 4.6 13.7 - - + +
1414D PRO 2.7 21.0 + - - +
1415D LEU* 3.5 8.5 - - - +
1417D THR* 1.3 71.4 - - - +
1419D ARG* 1.3 63.4 + - - +
1421D ARG* 3.0 17.0 + - - +
1422D LEU* 3.0 15.1 + - - +
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Residues in contact with ARG1419 (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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510D LYS* 5.5 4.5 - - + -
511D LEU* 3.9 24.2 - - + +
1392D PHE 5.9 1.1 - - - -
1393D PHE* 4.6 28.7 + - + +
1415D LEU 2.9 20.2 + - - +
1416D HIS* 4.3 3.6 - - - +
1418D LEU* 1.3 74.1 - - - +
1420D SER* 1.3 58.3 + - - +
1422D LEU* 3.0 31.5 + - - +
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Residues in contact with SER1420 (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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511D LEU* 4.0 12.0 - - - +
1416D HIS 2.9 21.9 + - - -
1417D THR* 3.9 5.6 - - - -
1419D ARG* 1.3 77.8 - - - +
1421D ARG* 1.3 59.4 + - - +
1422D LEU 3.2 3.5 + - - +
1498D ARG* 5.7 5.0 - - - +
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Residues in contact with ARG1421 (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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1417D THR 2.9 19.0 + - - +
1418D LEU* 3.0 7.1 + - - +
1420D SER* 1.3 75.3 - - - +
1422D LEU* 1.3 57.5 + - - +
1423D SER 4.1 1.2 + - - -
1498D ARG* 5.6 2.3 - - - +
1500D THR* 4.5 13.9 - - - -
1501D SER* 4.9 6.1 + - - -
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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