Contacts of the helix formed by residues 632 - 638 (chain A) in PDB entry 2CFZ
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 LEU 632 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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561A LEU* 3.8 25.0 - - + +
562A SER 4.2 8.1 - - - +
563A ILE* 3.8 11.2 - - + -
595A GLY* 3.6 40.8 - - - +
596A GLN* 3.2 13.9 - - + +
629A ASN* 3.8 27.1 - - + +
631A LEU* 1.3 77.9 - - - +
633A LEU* 1.3 59.0 + - - +
635A GLN* 3.2 27.4 + - - +
636A LEU* 2.8 30.5 + - - +
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Residues in contact with LEU 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563A ILE* 3.6 22.4 - - + -
565A LEU* 5.1 9.2 - - + -
576A LEU* 5.2 7.4 - - + -
596A GLN* 2.9 22.8 - - - +
598A VAL* 4.2 28.7 - - + -
608A LEU* 6.3 1.1 - - + -
624A LEU* 4.8 15.5 - - + -
630A PRO 5.3 1.1 - - - +
631A LEU 3.4 0.4 - - - -
632A LEU* 1.3 76.6 - - - +
634A GLY* 1.3 58.9 + - - +
636A LEU* 3.5 5.0 + - + +
637A PHE* 3.0 64.2 + - + -
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Residues in contact with GLY 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630A PRO 5.1 1.6 + - - -
631A LEU* 3.4 7.1 + - - -
632A LEU 3.2 0.6 - - - -
633A LEU* 1.3 78.2 - - - +
635A GLN* 1.3 58.7 + - - +
637A PHE* 3.4 8.1 + - - +
638A GLY* 2.9 26.7 + - - -
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Residues in contact with GLN 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561A LEU* 4.1 9.8 - - + +
629A ASN* 5.0 2.3 + - - -
631A LEU* 3.0 37.8 + - + +
632A LEU* 3.4 32.3 - - - +
634A GLY* 1.3 75.7 - - - +
636A LEU* 1.3 62.6 + - - +
638A GLY* 3.1 11.9 + - - -
639A MET* 3.4 26.8 + - + +
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Residues in contact with LEU 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A LEU* 6.3 0.9 - - + -
551A LEU* 4.4 16.6 - - + -
561A LEU* 4.2 18.0 - - + +
563A ILE* 4.4 10.5 - - + -
576A LEU* 4.4 19.7 - - + -
578A LEU* 4.7 11.9 - - + -
583A LEU* 4.1 42.4 - - + -
632A LEU 2.8 18.8 + - - +
633A LEU* 3.5 8.3 - - + +
635A GLN* 1.3 72.0 - - - +
637A PHE* 1.3 75.2 + - + +
639A MET* 3.1 22.0 + - - +
640A LEU* 3.8 9.8 + - + +
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Residues in contact with PHE 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544A PHE* 6.4 1.3 - + - -
547A LEU* 4.1 24.0 - - + -
576A LEU* 6.3 0.9 - - + -
605A LEU* 4.9 15.0 - - + -
608A LEU* 5.1 14.6 - - + -
609A LEU* 5.3 8.3 - - + -
633A LEU* 3.0 53.8 + - + +
634A GLY* 3.9 7.2 - - - +
636A LEU* 1.3 86.9 - - + +
638A GLY* 1.3 59.9 + - - +
640A LEU* 3.2 38.6 + - + +
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Residues in contact with GLY 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555A ALA* 5.3 1.6 - - - +
634A GLY 2.9 14.8 + - - -
635A GLN* 3.1 7.3 + - - -
637A PHE* 1.3 76.0 - - - +
639A MET* 1.3 57.7 + - - +
640A LEU 3.3 4.4 + - - +
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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