Contacts of the helix formed by residues 633 - 640 (chain A) in PDB entry 3FZP
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 ASP 633 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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629A LEU* 4.0 20.9 - - + +
630A GLU* 3.0 32.1 + - - +
631A ASN 2.9 0.6 + - - -
632A LYS* 1.3 82.4 - - - +
634A VAL* 1.3 63.3 + - - +
635A ILE 3.5 0.4 - - - -
636A GLY* 3.6 4.8 + - - -
637A VAL* 3.3 24.2 + - + +
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Residues in contact with VAL 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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589A ILE* 4.0 23.3 - - + +
590A LYS* 3.8 27.4 - - + -
592A MET 5.6 0.2 - - - +
597A ILE* 4.1 2.5 - - + -
626A PHE* 4.3 19.7 - - + -
629A LEU* 4.3 17.3 - - + -
630A GLU 3.9 9.2 - - - +
631A ASN* 3.2 17.3 + - - +
633A ASP* 1.3 75.1 - - - +
635A ILE* 1.3 67.8 + - - +
637A VAL* 2.9 6.1 + - - +
638A LEU* 2.9 40.7 + - + +
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Residues in contact with ILE 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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589A ILE* 5.5 0.2 - - - +
594A PRO* 4.1 20.0 - - + -
597A ILE* 3.8 28.6 - - + +
598A ASN* 3.6 38.6 - - - +
631A ASN 4.7 1.0 + - - +
632A LYS 4.1 15.3 - - - +
634A VAL* 1.3 80.8 - - - +
636A GLY* 1.3 68.2 + - - +
638A LEU* 3.1 8.0 + - + +
639A GLU* 2.6 50.4 + - + +
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Residues in contact with GLY 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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633A ASP 3.6 5.6 + - - -
634A VAL 3.2 1.0 - - - -
635A ILE* 1.3 87.4 - - - +
637A VAL* 1.3 61.4 + - - +
639A GLU* 3.7 9.1 - - - +
640A LYS* 3.3 33.7 + - - +
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Residues in contact with VAL 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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626A PHE* 4.1 26.0 - - + -
628A TRP* 6.0 0.9 - - - +
629A LEU* 3.6 26.5 - - + -
633A ASP* 3.3 16.5 + - + +
634A VAL 2.9 8.4 + - - +
636A GLY* 1.3 75.0 - - - +
638A LEU* 1.3 64.3 + - - +
640A LYS* 3.3 24.3 - - - +
642A ASP* 3.2 42.6 + - + +
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Residues in contact with LEU 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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592A MET 4.0 13.7 - - - +
594A PRO* 4.5 14.4 - - + -
597A ILE* 4.1 9.4 - - + -
609A TRP* 3.7 34.1 - - + -
626A PHE* 4.0 22.7 - - + -
634A VAL* 2.9 32.9 + - + +
635A ILE* 3.4 12.6 - - + +
637A VAL* 1.3 74.4 - - - +
639A GLU* 1.3 57.8 + - - +
641A GLY* 2.7 23.7 + - - -
642A ASP 3.8 14.4 - - - +
643A ARG* 2.9 24.4 + - - +
664A TYR* 4.8 4.7 - - - -
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Residues in contact with GLU 639 (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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598A ASN* 3.3 16.6 + - - +
635A ILE* 2.6 40.1 + - + +
636A GLY* 3.7 8.7 - - - +
638A LEU* 1.3 73.1 - - - +
640A LYS* 1.3 59.7 + - - +
641A GLY 3.4 0.9 + - - -
664A TYR* 2.9 39.5 + - - -
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Residues in contact with LYS 640 (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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636A GLY* 3.3 18.0 + - - +
637A VAL* 3.3 25.1 - - - +
638A LEU 3.1 0.2 - - - -
639A GLU* 1.3 78.6 - - - +
641A GLY* 1.3 58.5 + - - +
642A ASP* 3.5 20.7 + - - +
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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