Contacts of the helix formed by residues 666 - 675 (chain A) in PDB entry 7ACN
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 ARG 666 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A ILE* 3.6 14.8 - - - +
180A GLY 3.0 24.7 + - - +
181A VAL* 4.5 6.7 - - - +
185A ASP* 5.5 1.8 + - - -
195A TRP* 4.7 1.6 - - - -
197A LEU* 4.0 21.5 - - + +
198A LYS* 6.4 1.8 - - + -
234A THR* 4.7 15.7 - - + +
235A GLY* 5.4 5.4 - - - +
264A GLY 5.2 8.0 + - - +
265A ALA 4.8 2.4 + - - -
266A THR* 3.5 45.7 + - - +
664A PHE 3.8 1.8 + - - -
665A ALA* 1.3 68.0 - - - +
667A ILE* 1.3 97.0 + - + +
669A GLU* 3.3 8.9 + - - +
670A THR* 3.1 32.5 + - - +
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Residues in contact with ILE 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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166A SER* 4.3 15.7 - - - +
180A GLY* 3.7 15.0 - - - +
181A VAL* 4.3 2.0 - - - -
182A GLY 4.1 8.7 - - - +
641A GLY 4.9 5.2 - - - +
642A SER 5.5 1.1 - - - +
643A SER* 3.5 39.3 - - - +
665A ALA* 3.5 1.8 - - - +
666A ARG* 1.3 108.5 - - + +
668A HIS* 1.3 63.3 + - - +
670A THR* 3.1 8.6 + - - +
671A ASN* 2.9 39.1 + - - +
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Residues in contact with HIS 668 (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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567A THR* 4.3 6.6 - - + +
570A ILE* 4.0 3.7 - - + +
638A TYR* 3.5 41.7 + + - +
639A GLY* 3.8 32.8 + - - +
642A SER 5.9 0.6 + - - -
644A ARG 5.3 0.8 + - - -
647A SER* 3.5 45.3 + - - -
648A ALA* 4.1 2.1 + - - -
659A ILE* 5.9 0.2 - - - +
664A PHE* 4.4 1.1 - + - -
665A ALA* 3.5 6.1 + - - +
666A ARG 3.3 0.6 - - - -
667A ILE* 1.3 77.4 - - - +
669A GLU* 1.3 58.2 + - - +
671A ASN* 3.3 10.6 + - - +
672A LEU* 2.9 54.6 + - + +
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Residues in contact with GLU 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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664A PHE* 3.8 26.4 - - + +
665A ALA 3.2 17.4 + - - +
666A ARG* 3.7 7.7 - - - +
667A ILE 3.3 0.2 - - - -
668A HIS* 1.3 77.0 - - - +
670A THR* 1.3 61.5 + - - +
672A LEU* 3.4 11.5 + - - +
673A LYS* 3.2 33.6 + - - +
679A PRO* 3.9 22.7 - - + +
729A HIS* 5.6 0.2 - - - -
730A THR* 2.8 37.8 + - - +
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Residues in contact with THR 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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185A ASP* 3.6 31.4 - - - +
196A GLU 5.9 2.5 - - - +
666A ARG* 3.1 23.2 + - - +
667A ILE* 3.6 9.6 - - - -
669A GLU* 1.3 76.6 - - - +
671A ASN* 1.3 59.3 + - - +
673A LYS* 3.2 14.3 + - + +
674A LYS* 2.9 32.3 + - + +
735A GLN* 6.2 1.8 - - - +
738A TRP* 5.0 7.9 - - + -
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Residues in contact with ASN 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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182A GLY* 3.4 26.3 - - - +
184A ALA* 5.7 1.8 - - - +
185A ASP* 5.0 4.0 + - - -
643A SER 2.9 25.6 - - - +
644A ARG 4.1 1.2 - - - +
645A GLU* 3.6 20.1 + - + +
648A ALA* 3.6 15.0 - - + -
667A ILE* 2.9 26.9 + - - +
668A HIS* 3.6 13.6 + - - +
670A THR* 1.3 75.9 - - - +
672A LEU* 1.4 61.7 + - - +
674A LYS* 3.2 10.5 + - - +
675A GLN* 3.2 26.9 + - - +
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Residues in contact with LEU 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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647A SER 4.7 1.6 - - - +
648A ALA* 3.8 14.4 - - + -
651A PRO* 4.9 0.7 - - + -
659A ILE* 4.0 23.1 - - + -
664A PHE* 3.6 22.0 - - + -
668A HIS* 2.9 44.1 + - + +
669A GLU* 3.6 5.4 - - - +
670A THR 3.3 0.2 - - - -
671A ASN* 1.4 75.1 - - - +
673A LYS* 1.3 60.7 + - - +
675A GLN* 3.4 6.9 + - - +
677A LEU* 3.1 51.4 + - + +
679A PRO* 3.5 29.6 - - + -
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Residues in contact with LYS 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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61A TYR* 3.2 7.9 + - - -
669A GLU* 3.2 31.9 + - - +
670A THR* 3.2 11.9 + - - +
672A LEU* 1.3 76.1 - - - +
674A LYS* 1.3 64.5 + - - +
676A GLY* 3.2 12.8 + - - -
677A LEU 4.0 8.1 - - - -
679A PRO* 3.6 5.6 - - + -
730A THR* 2.9 32.0 + - - -
731A PHE* 3.6 37.7 - - + -
735A GLN* 2.8 37.4 + - + +
738A TRP* 3.6 27.6 - - + +
739A PHE* 4.8 1.2 + - - +
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Residues in contact with LYS 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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184A ALA* 3.9 27.2 + - + +
185A ASP* 3.1 28.9 - - - +
188A ASP* 2.7 37.5 + - - -
670A THR* 2.9 18.8 + - + +
671A ASN* 3.2 16.1 + - - +
673A LYS* 1.3 77.4 - - - +
675A GLN* 1.3 63.1 + - - +
676A GLY 3.3 0.2 - - - -
738A TRP* 3.6 35.6 - - + -
743A SER* 3.4 3.5 - - - -
744A ALA* 2.8 49.9 + - + +
745A LEU 4.7 0.2 + - - -
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Residues in contact with GLN 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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82A GLN* 3.5 20.9 + - - +
184A ALA* 4.1 6.9 - - - +
544A PHE* 3.4 17.4 - - + -
645A GLU* 3.9 12.1 - - + +
648A ALA* 4.0 26.7 - - + +
649A LEU* 3.4 35.6 - - + +
652A ARG* 2.9 31.7 + - + +
671A ASN* 3.2 17.5 + - + +
672A LEU 3.4 3.8 + - - +
673A LYS 3.2 0.6 - - - -
674A LYS* 1.3 84.1 + - - +
676A GLY* 1.3 58.5 + - - +
677A LEU* 3.4 4.2 + - + -
742A GLY 3.6 6.1 - - - +
743A SER* 4.1 5.6 - - - -
745A LEU* 6.1 1.4 - - - +
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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