Contacts of the helix formed by residues 665 - 677 (chain A) in PDB entry 5ID6
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 665 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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621A PHE 5.5 1.1 - - - +
622A LYS 6.5 0.4 - - - -
623A LYS* 3.2 40.7 + - - -
627A PHE* 4.6 5.8 - - + -
632A CYS* 4.0 11.0 - - - -
636A ILE* 5.3 0.3 - - - +
663A TYR* 3.8 17.3 - - - +
664A LYS* 1.3 83.6 + - - +
666A ILE* 1.3 63.4 + - + +
667A ALA* 3.7 20.0 - - - +
668A GLY* 3.6 16.0 + - - -
669A PHE* 4.0 2.1 + - - +
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Residues in contact with ILE 666 (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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621A PHE* 3.8 40.7 + - + +
622A LYS* 5.4 2.7 - - - -
632A CYS* 3.9 11.2 - - - -
635A LEU* 4.5 6.1 - - + -
636A ILE* 3.5 30.1 - - + -
639A PHE* 4.9 1.3 - - + -
665A ASP* 1.3 73.3 - - + +
667A ALA* 1.3 64.8 + - + +
668A GLY 3.1 2.2 - - - -
669A PHE* 3.2 4.6 + - + +
670A TYR* 3.0 71.3 + - + +
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Residues in contact with ALA 667 (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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665A ASP* 3.3 16.6 - - - +
666A ILE* 1.3 83.2 - - + +
668A GLY* 1.3 58.3 + - - +
670A TYR* 3.7 10.6 - - + +
671A ARG* 3.0 28.9 + - - +
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Residues in contact with GLY 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663A TYR* 3.6 18.7 - - - -
664A LYS 6.1 0.2 - - - -
665A ASP* 3.6 16.8 + - - -
666A ILE 3.1 1.0 - - - -
667A ALA* 1.3 81.0 - - - +
669A PHE* 1.3 62.2 + - - +
671A ARG* 3.6 11.0 + - - +
672A GLU* 3.6 17.7 + - - +
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Residues in contact with PHE 669 (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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593A LEU* 4.0 8.7 - - + -
636A ILE* 3.6 38.4 - - + -
639A PHE* 3.8 31.2 - + + -
640A LYS* 3.8 25.1 - - + -
643A ILE* 4.4 2.9 - - + -
657A PHE* 3.8 29.6 - + - -
663A TYR* 3.5 34.6 - + + -
665A ASP 4.0 0.6 + - - -
666A ILE* 3.2 9.4 + - + +
668A GLY* 1.3 74.4 - - - +
670A TYR* 1.3 76.7 + + - +
672A GLU* 3.2 5.2 + - - +
673A VAL* 3.1 38.7 + - + +
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Residues in contact with TYR 670 (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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589A PRO* 3.8 24.1 - - + +
590A ASN* 3.6 45.2 + - + +
593A LEU* 4.4 8.5 - - + -
594A PRO* 4.3 4.7 - - - +
616A TYR* 6.2 0.2 - - - -
621A PHE* 4.4 13.0 - + - -
635A LEU* 4.8 0.2 - - - +
639A PHE* 3.6 28.8 - + - -
666A ILE* 3.0 54.0 + - + +
667A ALA* 4.0 8.5 - - + +
669A PHE* 1.3 88.0 - + - +
671A ARG* 1.3 58.2 + - - +
673A VAL* 3.2 4.8 + - - +
674A GLU* 2.8 30.9 + - - +
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Residues in contact with ARG 671 (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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667A ALA 3.0 18.1 + - - +
668A GLY* 3.9 11.9 + - - +
669A PHE 3.2 0.2 - - - -
670A TYR* 1.3 76.2 - - - +
672A GLU* 1.3 65.9 + - - +
674A GLU* 3.2 12.7 + - - +
675A GLU* 2.6 66.1 + - - +
805A CYS* 3.9 26.7 + - + +
806A PRO* 3.6 22.8 + - + -
807A LYS* 3.9 27.1 - - - +
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Residues in contact with GLU 672 (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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656A ASN 4.8 5.2 - - - +
657A PHE* 4.0 14.4 - - + -
658A SER* 2.4 34.6 + - - -
663A TYR* 2.2 37.0 + - - -
668A GLY 3.6 8.7 + - - +
669A PHE 3.2 7.5 + - - +
671A ARG* 1.3 89.7 + - - +
673A VAL* 1.3 59.5 + - - +
675A GLU* 4.2 8.3 - - - +
676A GLN* 2.8 42.3 + - - +
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Residues in contact with VAL 673 (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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586A LEU* 4.0 21.9 - - + +
589A PRO* 3.7 22.7 - - + -
593A LEU* 4.2 13.5 - - + -
643A ILE* 4.7 2.0 - - + -
655A PHE* 4.1 10.2 - - + -
657A PHE* 3.7 15.9 - - + -
669A PHE* 3.1 45.6 + - + +
670A TYR* 3.2 7.6 + - - +
672A GLU* 1.3 75.2 - - - +
674A GLU* 1.3 55.4 + - - +
677A GLY* 2.6 36.7 + - - -
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Residues in contact with GLU 674 (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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586A LEU 5.1 7.4 - - - +
588A GLY* 5.0 5.5 + - - +
589A PRO* 3.6 27.5 - - + +
590A ASN* 5.6 1.1 - - - +
670A TYR 2.8 16.6 + - - +
671A ARG* 3.5 13.3 - - - +
673A VAL* 1.3 79.4 - - - +
675A GLU* 1.3 60.8 + - - +
677A GLY* 3.5 8.8 + - - +
737A ARG* 3.2 22.3 + - - +
804A LYS* 3.5 35.6 + - + +
805A CYS* 3.8 15.9 - - - -
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Residues in contact with GLU 675 (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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671A ARG* 2.6 51.4 + - - +
672A GLU* 3.7 7.6 - - - +
673A VAL 3.3 0.2 - - - -
674A GLU* 1.3 74.1 - - - +
676A GLN* 1.3 68.3 + - + +
678A TYR* 4.4 5.5 + - - +
735A GLN* 4.8 1.1 - - - +
737A ARG* 3.0 23.7 + - - +
805A CYS* 3.5 18.9 - - + +
807A LYS* 5.0 6.5 - - - +
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Residues in contact with GLN 676 (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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653A TYR* 3.5 15.2 - - - +
654A ASP 4.1 13.0 + - - +
655A PHE* 3.3 24.0 - - + -
656A ASN* 2.6 56.0 + - - +
657A PHE* 3.7 7.4 - - - -
672A GLU* 2.8 28.7 + - - +
675A GLU* 1.3 81.4 + - + +
677A GLY* 1.3 56.3 + - - +
678A TYR 2.8 20.0 + - - +
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Residues in contact with GLY 677 (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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585A LEU* 3.5 1.9 - - - +
586A LEU* 2.6 41.9 + - - +
653A TYR* 3.4 20.2 - - - -
655A PHE* 4.4 4.7 - - - -
673A VAL 2.6 24.2 + - - -
674A GLU* 3.5 4.2 + - - -
675A GLU 3.4 1.8 - - - -
676A GLN* 1.3 69.4 - - - +
678A TYR* 1.3 59.4 + - - +
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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