Contacts of the helix formed by residues 687 - 696 (chain B) in PDB entry 2P1U
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 HIS 687 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298A VAL* 4.0 15.0 - - + -
302A ARG* 3.3 53.4 + - - +
453A GLU* 3.4 24.6 - - + +
456A GLU* 3.2 29.8 + - + -
457A ALA 4.9 8.1 - - - -
458A PRO* 5.1 6.7 - - + +
688B LYS* 1.3 64.8 + - - +
690B LEU* 4.6 5.2 - - + -
691B HIS* 2.9 40.1 + - + -
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Residues in contact with LYS 688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A THR* 6.1 1.6 - - - +
453A GLU* 3.3 6.6 + - - +
687B HIS* 1.3 74.0 - - - +
689B ILE* 1.3 81.6 + - + +
691B HIS* 3.7 5.6 + - - +
692B ARG* 3.0 68.1 + - - +
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Residues in contact with ILE 689 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A PHE* 4.3 10.1 - - + -
449A THR* 3.6 45.8 - - - +
450A PHE* 3.9 19.3 - - + +
453A GLU* 2.8 23.4 + - + +
688B LYS* 1.3 92.2 - - + +
690B LEU* 1.3 57.8 + - - +
692B ARG* 3.2 9.8 + - - +
693B LEU* 3.0 50.8 + - + +
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Residues in contact with LEU 690 (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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280A VAL* 3.8 26.2 - - + -
298A VAL* 3.7 35.9 - - + +
301A LEU* 3.9 15.3 - - + -
302A ARG* 3.8 19.7 - - + -
450A PHE* 3.9 15.0 - - + -
453A GLU* 3.1 18.4 + - - +
454A MET* 4.2 12.1 - - + -
687B HIS* 4.1 4.9 - - + +
689B ILE* 1.3 73.8 - - - +
691B HIS* 1.3 66.1 + - - +
693B LEU* 3.3 2.2 + - - -
694B LEU* 3.0 47.5 + - + +
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Residues in contact with HIS 691 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A LEU* 3.7 24.9 - - + +
295A ASP* 4.2 17.9 - - - -
298A VAL* 3.7 30.9 - - + +
687B HIS* 2.9 43.9 + - + +
688B LYS* 3.9 5.6 - - - +
690B LEU* 1.3 77.3 - - - +
692B ARG* 1.3 64.0 + - + +
694B LEU* 3.9 4.4 - - - +
695B GLN* 3.0 26.6 + - - +
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Residues in contact with ARG 692 (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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688B LYS* 3.0 63.1 + - - +
689B ILE* 3.2 8.8 + - - +
691B HIS* 1.3 76.6 - - + +
693B LEU* 1.3 60.0 + - + +
695B GLN* 3.8 4.8 - - - +
696B ASP* 2.9 30.8 + - - +
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Residues in contact with LEU 693 (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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277A PHE* 3.6 29.4 - - + +
280A VAL* 3.9 21.6 - - + +
281A GLU* 4.7 5.9 - - - +
284A LYS* 2.9 23.0 + - - -
450A PHE* 3.5 32.1 - - + -
689B ILE* 3.0 26.1 + - + +
690B LEU 4.0 2.2 - - - +
692B ARG* 1.3 78.9 - - + +
694B LEU* 1.3 59.4 + - - +
696B ASP 3.2 16.0 - - - +
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Residues in contact with LEU 694 (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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280A VAL* 3.7 21.5 - - + +
284A LYS* 3.4 22.3 + - + +
289A PHE* 4.0 8.7 - - + -
294A LEU* 3.4 22.6 - - + +
297A GLN* 3.5 31.9 - - + +
298A VAL* 3.7 30.3 - - + +
301A LEU* 3.8 13.0 - - + -
690B LEU* 3.0 32.3 + - + +
691B HIS 4.0 0.2 - - - +
693B LEU* 1.3 76.5 - - - +
695B GLN* 1.3 65.4 + - - +
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Residues in contact with GLN 695 (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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284A LYS* 4.5 1.3 + - - -
294A LEU* 4.1 20.0 - - + +
691B HIS 3.0 18.6 + - - +
692B ARG* 3.8 5.2 - - - +
694B LEU* 1.3 78.2 - - - +
696B ASP* 1.3 65.6 + - + +
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Residues in contact with ASP 696 (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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281A GLU* 5.8 1.1 - - - -
284A LYS* 3.9 9.4 - - - +
692B ARG 2.9 19.6 + - - +
693B LEU* 3.2 27.2 - - - +
694B LEU 3.3 0.2 - - - -
695B GLN* 1.3 87.7 - - + +
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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