Contacts of the helix formed by residues 635 - 647 (chain A) in PDB entry 2PZI
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 635 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421A THR* 3.4 22.3 + - + +
424A VAL* 3.6 26.4 - - + +
603A ILE* 4.0 27.8 - - + -
607A PHE* 4.1 1.8 - - + -
629A VAL* 4.0 3.0 - - + +
633A SER* 3.0 8.0 - - - +
634A ARG* 1.3 79.3 + - + +
636A PHE* 1.3 57.3 + - - +
637A THR 3.5 0.9 - - - -
638A THR* 3.5 11.0 + - - -
639A ALA* 2.9 28.8 + - - +
757A GOL 3.2 25.7 + - - -
477B VAL* 4.0 15.6 - - + +
481B ASP* 3.5 21.7 + - - -
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Residues in contact with PHE 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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627A ASP 4.9 0.4 - - - -
629A VAL* 3.1 37.2 - - + -
630A PRO 3.8 6.1 - - - +
631A PRO* 3.7 36.6 - - + +
633A SER* 3.0 18.2 + - - +
634A ARG 3.3 0.4 - - - -
635A HIS* 1.3 76.2 - - - +
637A THR* 1.3 67.2 + - - +
639A ALA* 3.1 3.6 + - - +
640A ARG* 2.9 79.4 + - + +
671A LEU* 5.8 5.2 - - + -
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Residues in contact with THR 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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634A ARG 4.6 5.5 + - - -
635A HIS 3.5 0.2 - - - -
636A PHE* 1.3 82.8 - - - +
638A THR* 1.3 64.6 + - - +
640A ARG* 3.1 8.1 + - - +
641A LEU* 2.9 33.0 + - + +
671A LEU* 4.1 31.1 - - + +
675A GLU* 3.1 44.6 + - + -
676A PRO 5.3 0.2 - - - +
678A VAL* 5.1 0.2 - - + -
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Residues in contact with THR 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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424A VAL* 3.7 38.0 - - + +
425A ASP* 4.4 6.1 - - + +
428A VAL* 4.0 18.4 - - + -
607A PHE* 4.3 0.4 - - + -
634A ARG 4.8 3.3 + - - -
635A HIS* 3.5 16.6 + - - -
636A PHE 3.2 0.6 - - - -
637A THR* 1.3 79.5 - - - +
639A ALA* 1.3 50.0 + - - +
641A LEU* 3.3 10.9 + - - +
642A THR* 2.4 44.3 + - - +
677A ARG* 5.3 4.0 + - - -
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Residues in contact with ALA 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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607A PHE* 3.6 22.4 - - + -
626A LEU* 3.9 27.2 - - + +
629A VAL* 3.9 15.0 - - + -
635A HIS 2.9 18.1 + - - +
636A PHE* 3.4 5.2 - - + +
638A THR* 1.3 76.2 - - - +
640A ARG* 1.3 60.6 + - - +
642A THR* 3.5 4.2 + - - -
643A SER* 3.0 29.6 + - - -
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Residues in contact with ARG 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626A LEU 3.7 9.3 + - - -
627A ASP* 3.1 51.4 + - - +
636A PHE* 2.9 59.1 + - + +
637A THR* 3.1 12.3 + - - +
639A ALA* 1.3 75.3 + - - +
641A LEU* 1.3 63.8 + - - +
643A SER* 3.3 9.4 + - - -
644A ALA* 3.3 16.1 + - - +
667A ARG* 3.6 48.2 - - - +
671A LEU* 4.4 9.0 - - + -
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Residues in contact with LEU 641 (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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428A VAL* 3.9 11.9 - - + -
637A THR* 2.9 30.8 + - + +
638A THR* 3.7 7.0 - - - +
640A ARG* 1.3 72.4 - - - +
642A THR* 1.3 66.7 + - - +
644A ALA* 3.2 8.2 + - - +
645A VAL* 3.0 25.6 + - - +
668A VAL* 4.5 8.3 - - + -
671A LEU* 3.7 23.1 - - + -
676A PRO 4.0 8.5 - - - +
677A ARG* 3.8 36.3 - - + +
678A VAL* 4.3 9.6 - - + +
681A ILE* 3.8 30.2 - - + +
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Residues in contact with THR 642 (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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424A VAL 4.5 2.0 + - - +
427A LEU* 3.8 35.7 - - + -
428A VAL* 3.6 14.9 - - + +
607A PHE* 3.5 22.8 - - + -
610A ALA* 6.3 0.2 - - + -
626A LEU* 3.9 17.0 - - + -
638A THR* 2.4 36.1 + - - +
639A ALA 3.5 6.7 - - - -
641A LEU* 1.3 72.3 - - - +
643A SER* 1.3 55.3 + - - +
645A VAL* 3.2 3.8 + - - +
646A THR* 2.8 34.2 + - - +
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Residues in contact with SER 643 (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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623A VAL* 3.7 24.6 + - - +
626A LEU* 3.6 22.4 - - - +
627A ASP* 4.5 2.4 + - - -
639A ALA 3.0 15.3 + - - -
640A ARG* 3.4 12.4 + - - -
642A THR* 1.3 72.4 - - - +
644A ALA* 1.3 66.3 + - - +
646A THR* 3.2 3.4 + - - -
647A LEU* 3.0 30.2 + - - +
667A ARG* 3.4 23.5 + - - -
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Residues in contact with ALA 644 (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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640A ARG 3.3 7.3 + - - +
641A LEU* 3.2 11.2 + - - +
643A SER* 1.3 79.4 - - - +
645A VAL* 1.3 65.5 + - - +
647A LEU* 3.1 14.4 + - - +
648A LEU* 3.7 15.0 + - - +
664A ALA* 3.7 20.0 - - - +
667A ARG* 4.6 1.0 - - + +
668A VAL* 3.7 30.1 - - + -
681A ILE* 3.8 9.9 - - + -
684A LEU* 5.3 0.4 - - - -
685A VAL* 4.1 6.7 - - + -
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Residues in contact with VAL 645 (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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427A LEU* 3.4 27.1 - - + +
428A VAL* 3.9 13.7 - - + -
431A THR* 4.2 17.3 - - + -
641A LEU 3.0 16.8 + - - +
642A THR* 3.5 6.1 - - - +
644A ALA* 1.3 75.7 - - - +
646A THR* 1.3 61.1 + - - +
647A LEU 3.3 0.5 + - - -
648A LEU* 3.3 18.9 + - - +
681A ILE* 3.7 28.9 - - + -
684A LEU* 4.6 15.5 - - + +
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Residues in contact with THR 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A LEU* 3.7 28.9 - - + -
610A ALA* 6.1 1.1 - - + -
614A SER* 3.7 20.4 + - - +
619A ARG* 3.4 29.3 + - - +
622A ALA* 4.4 5.4 - - + +
623A VAL* 3.6 17.0 - - - +
626A LEU* 4.2 9.4 - - + -
642A THR* 2.8 33.8 + - + +
643A SER 3.6 4.5 + - - -
645A VAL* 1.3 73.0 - - - +
647A LEU* 1.3 61.2 + - - +
648A LEU 3.1 4.8 + - - +
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Residues in contact with LEU 647 (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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619A ARG* 3.5 30.4 + - + +
620A VAL* 5.8 4.3 - - + -
623A VAL* 3.6 29.8 - - + -
643A SER 3.0 20.7 + - - +
644A ALA 3.1 6.8 + - - +
646A THR* 1.3 77.6 - - - +
648A LEU* 1.3 70.2 + - + +
656A VAL* 4.4 3.8 - - - +
660A GLN* 3.9 31.4 - - + +
663A ASP* 3.7 15.9 - - + +
664A ALA* 3.6 37.9 - - + +
667A ARG* 4.8 2.9 - - - -
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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