Contacts of the helix formed by residues 745 - 751 (chain D) in PDB entry 1NYE
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 CYS 745 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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676D HIS* 4.4 3.8 - - - -
679D CYS* 3.8 11.4 - - - +
680D PHE* 3.8 24.7 - - - -
683D ALA* 3.5 27.5 - - + +
741D ALA* 2.9 17.6 + - - +
742D LYS 4.4 0.2 - - - -
743D ALA 3.7 0.2 - - - -
744D GLY* 1.3 72.2 - - - +
746D PRO* 1.3 78.2 - - + +
748D SER* 3.0 44.5 + - - -
749D GLN* 3.1 10.0 + - - +
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Residues in contact with PRO 746 (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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459C ARG* 4.3 9.4 - - - +
460C PHE* 6.0 2.7 - - + -
469C GLU* 4.7 2.5 - - - +
506C LEU* 4.1 20.2 - - + -
513C PHE* 3.9 35.7 - - + +
514C ALA* 5.0 1.1 - - - -
515C ILE* 4.4 9.2 - - + +
679D CYS* 3.3 20.4 - - - +
683D ALA* 5.2 3.1 - - + -
744D GLY 3.6 2.8 - - - +
745D CYS* 1.3 80.7 - - + +
747D VAL* 1.3 65.3 + - - +
749D GLN* 3.0 14.4 + - + +
750D VAL* 2.9 22.2 + - + +
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Residues in contact with VAL 747 (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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468C PRO* 4.1 9.4 - - + -
472C ILE* 3.9 26.9 - - + -
515C ILE* 4.6 5.6 - - + +
672D ILE* 5.0 2.0 - - + +
675D ALA 4.0 7.6 - - - +
676D HIS* 3.4 40.4 - - + +
679D CYS* 3.3 29.5 - - + -
745D CYS 3.2 1.0 + - - -
746D PRO* 1.3 74.6 - - - +
748D SER* 1.3 64.9 + - - +
750D VAL* 3.0 17.5 + - - +
751D LEU* 3.2 25.7 + - + +
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Residues in contact with SER 748 (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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676D HIS* 2.9 28.5 + - - -
720D LEU* 5.0 0.3 - - - +
742D LYS 2.4 29.6 + - - -
743D ALA* 3.9 11.7 - - - -
745D CYS* 3.0 18.4 + - - -
747D VAL* 1.3 77.7 - - - +
749D GLN* 1.3 62.8 + - - +
751D LEU* 3.1 24.6 + - - +
755D ILE* 4.6 11.0 - - - +
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Residues in contact with GLN 749 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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513C PHE 5.4 4.7 - - - +
514C ALA* 5.7 6.5 - - + -
552C LYS* 3.0 44.5 + - - +
743D ALA 3.4 16.6 + - - +
744D GLY* 3.4 28.6 + - - +
745D CYS 3.1 6.4 + - - +
746D PRO* 3.0 13.4 + - + +
748D SER* 1.3 76.4 - - - +
750D VAL* 1.3 57.7 + - + +
751D LEU 3.4 2.0 + - - +
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Residues in contact with VAL 750 (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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472C ILE* 5.7 2.5 - - + -
514C ALA* 6.1 0.2 - - + -
515C ILE* 3.4 46.9 - - + +
550C VAL 3.4 3.3 - - - +
551C LEU* 3.4 24.3 - - + +
552C LYS* 2.9 34.4 + - + +
553C ALA* 4.1 20.4 - - + +
746D PRO 2.9 18.8 - - - +
747D VAL* 3.0 7.0 + - - +
749D GLN* 1.3 78.4 - - + +
751D LEU* 1.3 62.3 + - + +
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Residues in contact with LEU 751 (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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472C ILE* 6.1 2.7 - - + -
550C VAL* 3.4 33.0 - - + +
551C LEU* 4.5 10.1 - - + -
552C LYS* 5.4 2.3 - - - +
672D ILE* 4.3 18.6 - - + -
676D HIS* 4.0 8.7 - - + +
715D ILE* 5.8 0.7 - - + -
718D ILE* 3.3 31.9 - - + -
747D VAL* 3.2 32.5 + - + +
748D SER 3.1 14.4 + - - +
749D GLN 4.7 2.4 - - - +
750D VAL* 1.3 81.8 - - + +
752D LYS* 1.3 60.6 + - - +
753D ALA* 3.1 12.7 + - + +
755D ILE* 4.5 8.4 - - + +
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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