Contacts of the helix formed by residues 618 - 628 (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 ASP 618 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613A ARG* 3.0 41.2 + - + +
616A GLU* 3.1 18.6 + - - +
617A GLY* 1.3 72.5 - - - +
619A ARG* 1.3 60.0 + - - +
620A VAL* 3.6 8.1 + - - +
621A GLY* 2.7 33.7 + - - -
622A ALA* 3.4 12.0 + - - +
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Residues in contact with ARG 619 (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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614A SER* 4.4 16.4 - - - +
617A GLY* 3.0 19.7 + - - +
618A ASP* 1.3 75.8 - - - +
620A VAL* 1.3 62.3 + - + +
621A GLY 3.5 0.2 - - - -
622A ALA* 3.9 7.3 - - - +
623A VAL* 3.4 28.8 + - - +
646A THR* 3.4 25.2 + - - +
647A LEU* 3.5 24.5 + - + +
648A LEU 4.8 7.2 - - - -
656A VAL* 3.8 25.4 - - - +
660A GLN* 2.8 35.8 + - - +
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Residues in contact with VAL 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A ASP* 3.1 6.7 - - - +
619A ARG* 1.3 79.9 - - + +
621A GLY* 1.3 59.5 + - - +
623A VAL* 3.5 4.7 + - - +
624A ARG* 3.0 31.9 + - + +
647A LEU* 5.8 4.0 - - + -
660A GLN* 5.2 15.3 - - + +
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Residues in contact with GLY 621 (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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613A ARG* 3.0 26.1 + - - -
618A ASP* 2.7 30.9 + - - -
620A VAL* 1.3 73.0 - - - +
622A ALA* 1.3 55.7 + - - +
624A ARG* 3.2 10.2 - - - +
625A THR* 2.8 30.0 + - - -
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Residues in contact with ALA 622 (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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610A ALA* 3.4 37.8 - - + +
613A ARG* 3.8 4.9 - - + +
614A SER* 3.9 13.7 - - - +
618A ASP 3.4 17.1 + - - +
619A ARG 3.9 5.4 - - - +
621A GLY* 1.3 76.8 - - - +
623A VAL* 1.3 56.6 + - - +
625A THR* 3.3 2.8 + - - -
626A LEU* 2.8 36.1 + - + +
646A THR* 4.4 7.0 - - + +
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Residues in contact with VAL 623 (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 3.4 19.6 + - - +
620A VAL* 3.9 4.7 - - - +
621A GLY 3.3 0.4 - - - -
622A ALA* 1.3 72.1 - - - +
624A ARG* 1.3 61.2 + - - +
626A LEU* 3.7 1.1 - - - +
627A ASP* 2.9 30.7 + - - +
643A SER* 3.7 18.4 - - - +
646A THR* 3.6 17.5 - - - +
647A LEU* 3.6 28.3 - - + -
663A ASP* 6.1 0.7 - - + +
667A ARG* 3.6 39.0 - - - +
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Residues in contact with ARG 624 (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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613A ARG* 3.1 37.8 - - - +
620A VAL* 3.0 19.7 + - + +
621A GLY* 3.2 12.6 - - - +
623A VAL* 1.3 78.7 - - - +
625A THR* 1.3 62.5 + - - +
627A ASP* 3.3 16.9 + - - +
628A GLU* 3.4 37.3 + - - +
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Residues in contact with THR 625 (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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596A TRP* 3.9 9.6 + - - +
606A ALA* 3.2 35.0 - - - +
609A LEU* 3.4 26.1 - - + +
610A ALA* 4.2 2.5 - - + +
613A ARG* 2.8 33.6 + - - -
621A GLY 2.8 12.6 + - - -
622A ALA* 3.5 7.4 - - - -
624A ARG* 1.3 74.6 + - - +
626A LEU* 1.3 63.5 + - - +
628A GLU* 3.1 29.1 + - - +
629A VAL* 4.1 2.9 + - - +
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Residues in contact with LEU 626 (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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606A ALA 4.4 5.2 - - - +
607A PHE* 3.6 44.4 - - + -
610A ALA* 3.8 20.4 - - + -
622A ALA 2.8 25.9 + - - +
623A VAL* 3.3 0.6 + - - +
625A THR* 1.3 73.5 - - - +
627A ASP* 1.3 61.9 + - - +
629A VAL* 3.3 24.5 + - + +
639A ALA* 3.9 12.4 - - + +
640A ARG* 3.7 9.1 + - - -
642A THR* 3.9 22.9 - - + -
643A SER* 3.6 32.1 - - - +
646A THR* 4.2 8.7 - - + -
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Residues in contact with ASP 627 (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* 2.9 26.8 + - - +
624A ARG* 3.4 11.1 - - - +
625A THR 3.2 0.4 - - - -
626A LEU* 1.3 75.7 - - - +
628A GLU* 1.3 58.8 + - + +
629A VAL 3.2 9.4 + - - +
636A PHE* 4.9 0.5 - - - -
640A ARG* 3.1 40.4 + - - +
643A SER* 4.5 0.9 + - - -
667A ARG* 3.0 35.2 + - - -
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Residues in contact with GLU 628 (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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596A TRP* 2.8 49.8 + - + +
600A ASP* 4.4 8.9 - - + +
624A ARG* 3.4 38.0 + - - +
625A THR* 3.1 13.3 + - - +
627A ASP* 1.3 76.2 - - + +
629A VAL* 1.3 62.6 + - - +
630A PRO* 3.3 8.1 - - - +
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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