Contacts of the helix formed by residues 623 - 633 (chain A) in PDB entry 5P9H
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 SER 623 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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591A TYR* 5.3 0.8 - - - -
618A ARG* 5.9 0.2 - - - +
621A LEU 3.8 3.8 + - - -
622A ALA* 1.4 76.6 - - - +
624A GLU* 1.3 69.5 + - - +
625A LYS* 3.4 10.8 + - - +
626A VAL* 3.9 19.6 - - - +
627A TYR* 3.3 19.4 + - - +
654A VAL* 6.4 0.9 - - - -
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Residues in contact with GLU 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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623A SER* 1.3 76.4 + - - +
625A LYS* 1.3 53.8 + - - +
627A TYR* 3.5 7.4 + - - +
628A THR* 2.8 36.2 + - - -
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Residues in contact with LYS 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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623A SER* 3.4 9.5 + - - +
624A GLU* 1.3 78.4 - - - +
626A VAL* 1.4 61.0 + - - +
628A THR* 3.5 14.5 - - - -
629A ILE* 3.5 19.4 - - - +
654A VAL* 4.0 21.1 - - + +
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Residues in contact with VAL 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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587A MET* 3.8 10.9 - - + +
591A TYR* 4.5 27.4 - - + +
622A ALA* 4.8 3.6 - - + -
623A SER* 3.7 24.6 + - - +
624A GLU 3.4 0.6 - - - -
625A LYS* 1.4 74.6 - - - +
627A TYR* 1.3 64.6 + - - +
629A ILE* 3.3 22.5 + - - +
630A MET* 3.3 13.1 + - + +
654A VAL* 4.8 11.5 - - + +
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Residues in contact with TYR 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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616A LEU 2.7 22.9 + - - -
617A TYR* 3.4 24.7 - - - -
618A ARG* 3.7 30.3 - - + -
619A PRO* 4.0 0.9 - - + -
622A ALA* 4.7 4.0 - - + +
623A SER 3.3 19.5 + - - +
624A GLU* 3.8 6.7 - - - +
625A LYS 3.4 0.2 - - - -
626A VAL* 1.3 72.3 - - - +
628A THR* 1.3 56.0 + - - +
629A ILE 3.2 0.7 - - - -
630A MET* 3.3 23.4 + - + +
631A TYR* 2.8 63.9 + + + +
634A TRP* 4.2 11.9 - + - -
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Residues in contact with THR 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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624A GLU 2.8 21.1 + - - -
625A LYS* 3.5 14.2 - - - -
626A VAL 3.3 0.2 - - - -
627A TYR* 1.3 75.3 - - - +
629A ILE* 1.4 58.7 + - + +
631A TYR* 4.0 5.2 - - - +
632A SER* 3.1 28.7 + - - -
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Residues in contact with ILE 629 (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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587A MET* 3.9 19.1 - - + -
625A LYS 3.5 10.8 - - - +
626A VAL* 3.3 11.9 + - - +
627A TYR 3.2 0.4 - - - -
628A THR* 1.4 75.8 - - + +
630A MET* 1.4 64.5 + - - +
632A SER* 2.7 23.2 + - - -
633A CYS* 3.6 9.0 - - - -
647A LEU* 3.7 21.5 - - + -
650A ASN* 3.5 50.3 - - + +
651A ILE* 3.9 16.4 - - + +
654A VAL* 3.6 20.6 - - + -
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Residues in contact with MET 630 (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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584A GLY* 3.6 20.8 - - - +
587A MET* 3.9 34.5 - - + +
588A TRP* 4.0 31.9 - - - -
591A TYR* 4.3 10.3 - - + -
619A PRO* 4.1 4.3 - - + -
622A ALA* 4.2 19.5 - - + -
626A VAL 3.3 17.2 + - - +
627A TYR* 3.3 37.7 + - + +
629A ILE* 1.4 78.4 - - - +
631A TYR* 1.4 61.0 + - - +
633A CYS* 3.5 11.5 - - - +
634A TRP* 3.3 26.0 - - + -
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Residues in contact with TYR 631 (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 GLY 5.6 1.7 + - - -
615A ARG* 3.9 26.0 - - + +
627A TYR* 2.8 58.5 + + + +
628A THR* 4.0 6.5 - - - +
630A MET* 1.4 70.7 - - - +
632A SER* 1.4 57.4 + - - +
633A CYS 3.1 4.5 - - - -
634A TRP* 2.9 45.1 + + + +
635A HIS* 4.0 0.7 + - - -
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Residues in contact with SER 632 (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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628A THR* 3.1 17.6 + - - -
629A ILE* 2.7 20.3 + - - -
631A TYR* 1.4 74.8 - - - +
633A CYS* 1.4 58.2 + - - +
634A TRP 3.3 0.4 + - - -
635A HIS* 4.0 7.4 + - - +
640A GLU 4.7 1.2 - - - +
641A ARG* 3.6 10.6 - - - +
642A PRO* 3.2 35.1 - - - +
647A LEU* 3.9 4.3 - - - +
650A ASN* 4.9 4.1 + - - -
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Residues in contact with CYS 633 (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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580A ILE* 3.3 32.5 - - - +
581A TRP* 3.5 14.4 + - - -
583A PHE* 4.4 4.3 - - - -
584A GLY* 4.0 19.5 - - - -
629A ILE 3.6 16.4 - - - -
630A MET* 3.5 10.1 - - - +
631A TYR 3.1 0.2 - - - -
632A SER* 1.4 75.1 - - - +
634A TRP* 1.3 60.2 + - + +
635A HIS 3.5 1.3 - - - -
641A ARG* 3.2 20.6 - - - -
642A PRO* 4.3 0.9 - - - -
647A LEU* 3.7 30.5 - - - -
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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