Contacts of the helix formed by residues 632 - 638 (chain A) in PDB entry 1PS9
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A VAL* 4.4 9.6 - - + -
448A VAL* 3.6 31.2 - - + +
449A THR* 4.2 11.0 - - - +
450A ALA* 4.1 16.2 - - + +
461A LEU* 3.5 31.5 - - + +
630A ARG 2.8 1.6 + - - -
631A ALA* 1.3 93.1 - - + +
633A ALA* 1.3 65.3 + - - +
634A GLN 3.4 1.6 - - - -
635A PRO* 3.6 7.9 - - + -
636A LEU* 2.9 39.7 + - + +
701A FAD 3.8 18.2 - - - +
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Residues in contact with ALA 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A LEU* 3.4 15.7 - - + +
630A ARG* 2.7 47.6 + - + +
632A LEU* 1.3 74.6 - - - +
634A GLN* 1.3 65.2 + - + +
636A LEU* 3.8 3.2 - - - +
637A ILE* 3.3 28.0 + - + +
643A VAL* 5.2 3.6 - - - +
645A LEU* 4.6 11.9 - - + -
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Residues in contact with GLN 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 ARG 4.3 0.4 + - - -
633A ALA* 1.3 76.6 - - + +
635A PRO* 1.3 62.6 - - + +
636A LEU 2.7 9.6 + - - -
637A ILE* 2.7 25.5 + - - +
638A ASP* 2.6 66.6 + - - +
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Residues in contact with PRO 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A ALA* 3.3 32.4 - - + +
630A ARG 4.9 0.4 - - - +
631A ALA 3.3 26.9 - - - +
632A LEU* 3.6 4.9 - - - +
634A GLN* 1.3 93.0 - - + +
636A LEU* 1.3 50.6 + - - +
638A ASP* 4.1 7.7 - - + +
639A SER* 2.5 30.2 + - - -
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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
----------------------------------------------------------
450A ALA* 3.9 25.6 - - + +
454A GLN* 5.3 2.9 - - + -
459A THR* 4.0 15.3 - - + +
461A LEU* 3.9 14.1 - - + -
632A LEU* 2.9 34.5 + - + +
633A ALA 3.8 2.2 - - - +
634A GLN 2.7 5.1 + - - -
635A PRO* 1.3 75.4 - - - +
637A ILE* 1.3 61.3 + - - +
638A ASP 3.3 0.9 - - - -
639A SER* 3.4 6.6 + - - -
641A LYS* 3.2 51.3 + - + +
643A VAL* 3.3 39.7 - - + -
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Residues in contact with ILE 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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633A ALA* 3.3 18.6 - - + +
634A GLN* 2.7 32.6 + - - +
636A LEU* 1.3 71.8 - - + +
638A ASP* 1.3 61.1 + - - +
639A SER 2.9 8.7 + - - -
640A GLY* 3.3 11.5 + - - +
641A LYS 4.6 8.7 - - - +
643A VAL* 5.3 6.5 - - + -
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Residues in contact with ASP 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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634A GLN* 2.6 51.1 + - - +
635A PRO* 4.2 5.5 - - + +
637A ILE* 1.3 72.3 - - - +
639A SER* 1.3 63.0 + - - +
640A GLY 3.7 0.9 - - - -
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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