Contacts of the helix formed by residues 571 - 579 (chain A) in PDB entry 2PWL
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 ASN 571 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300A ACP 3.7 24.9 + - - +
570A GLY* 1.3 76.0 - - - +
572A LEU* 1.3 64.5 + - - +
573A ARG* 3.2 10.7 + - - +
574A GLU* 2.9 40.8 + - - +
575A TYR* 3.0 17.3 + - - +
630A ARG* 3.2 36.1 + - - +
632A VAL 2.9 9.6 - - - +
633A LEU* 3.7 10.2 - - + +
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Residues in contact with LEU 572 (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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570A GLY 3.8 0.8 + - - -
571A ASN* 1.3 72.0 - - - +
573A ARG* 1.3 63.9 + - - +
575A TYR* 3.1 17.2 + - + +
576A LEU* 2.8 47.1 + - + +
606A CYS* 4.6 4.0 - - + -
610A LEU* 4.1 5.8 - - + -
629A ALA* 3.2 19.0 + - + +
632A VAL* 2.6 23.3 + - + +
633A LEU* 4.5 0.2 - - - +
634A VAL* 4.7 3.8 - - + +
640A MET* 3.1 37.5 - - + -
692A LEU* 4.4 2.0 - - + -
696A ILE* 3.7 31.4 - - + -
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Residues in contact with ARG 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A ASN* 3.2 9.0 + - - +
572A LEU* 1.3 78.3 - - - +
574A GLU* 1.3 58.8 + - - +
576A LEU* 3.5 1.6 + - - +
577A ARG* 2.8 64.9 + - - +
629A ALA* 3.4 21.2 + - + +
630A ARG* 4.1 15.9 - - - +
669A TRP* 4.9 5.1 - - - -
695A GLU* 3.5 20.0 + - - -
700A GLY* 3.5 25.7 + - - +
701A GLY 3.7 11.3 + - - -
702A SER* 2.7 31.5 + - - +
703A PRO* 4.7 2.8 - - - +
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Residues in contact with GLU 574 (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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569A LYS 5.6 1.6 - - - +
570A GLY* 5.6 1.8 - - - -
571A ASN* 2.9 27.3 + - - +
573A ARG* 1.3 74.2 - - - +
575A TYR* 1.3 67.9 + - - +
577A ARG* 3.3 7.0 + - - +
578A ALA* 3.1 26.2 + - - +
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Residues in contact with TYR 575 (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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569A LYS* 4.2 13.6 + - + +
571A ASN 3.0 12.7 + - - +
572A LEU* 3.3 26.2 - - + +
574A GLU* 1.3 79.0 - - - +
576A LEU* 1.3 67.1 + - + +
578A ALA* 4.9 0.2 - - - -
579A ARG* 2.8 73.5 + - - +
598A MET* 3.7 31.0 - - + +
606A CYS* 5.1 4.9 - - - -
634A VAL* 3.7 34.1 - - + -
638A ASN* 3.1 32.6 + - + +
640A MET* 5.7 0.9 - - - -
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Residues in contact with LEU 576 (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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572A LEU* 2.8 48.6 + - + +
573A ARG* 4.0 2.5 - - - +
575A TYR* 1.3 81.2 - - + +
577A ARG* 1.3 64.2 + - - +
579A ARG* 3.1 16.0 + - - +
580A ARG* 3.6 13.0 + - - +
598A MET* 3.7 35.7 - - + -
603A LEU* 4.2 10.3 - - + -
606A CYS* 5.2 2.0 - - - -
629A ALA* 5.5 1.6 - - + -
695A GLU 4.3 0.7 - - - +
696A ILE* 3.8 33.2 - - + +
699A LEU* 3.6 21.4 - - + +
700A GLY* 3.9 9.4 - - - +
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Residues in contact with ARG 577 (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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573A ARG* 2.8 56.1 + - - +
574A GLU* 3.3 6.0 + - - +
576A LEU* 1.3 75.9 - - - +
578A ALA* 1.3 59.9 + - - +
579A ARG 3.6 0.2 + - - -
580A ARG* 3.7 42.6 - - - +
699A LEU 3.6 15.9 - - - +
700A GLY* 3.5 20.0 + - - +
701A GLY* 6.1 0.2 - - - -
702A SER* 5.2 0.4 + - - -
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Residues in contact with ALA 578 (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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574A GLU 3.1 17.1 + - - +
575A TYR* 3.8 5.2 - - - +
577A ARG* 1.3 78.6 - - - +
579A ARG* 1.3 70.4 + - - +
580A ARG 3.4 4.7 + - - +
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Residues in contact with ARG 579 (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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569A LYS* 4.4 15.6 - - - +
575A TYR* 2.8 74.7 + - - +
576A LEU 3.1 8.0 + - - +
578A ALA* 1.3 90.6 - - - +
580A ARG* 1.3 58.8 + - - +
581A PRO* 3.7 3.3 - - - +
596A GLU* 3.6 36.1 + - - +
597A GLN* 3.5 17.9 - - - +
598A MET* 3.6 29.2 + - + +
638A ASN* 5.5 0.2 + - - -
699A LEU* 4.8 2.2 - - - +
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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