Contacts of the helix formed by residues 568 - 575 (chain C) in PDB entry 3GQL
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 568 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C GQL 6.0 1.8 - - - -
567C GLY* 1.3 74.3 - - - -
569C LEU* 1.3 64.1 + - - +
570C ARG* 2.7 36.5 + - - +
571C GLU* 3.1 36.3 + - - +
572C TYR* 2.9 23.8 + - - +
626C ALA 3.5 1.1 - - - +
627C ARG* 3.7 32.2 + - - +
629C VAL 3.1 15.3 - - - +
630C LEU* 3.9 9.8 - - + +
631C VAL* 4.3 1.6 - - - -
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Residues in contact with LEU 569 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568C ASN* 1.3 73.7 - - - +
570C ARG* 1.3 59.3 + - - +
572C TYR* 3.1 12.8 + - + +
573C LEU* 2.8 50.6 + - + +
603C CYS* 3.8 13.5 - - - -
607C VAL* 4.7 2.7 - - + -
626C ALA* 3.1 25.7 + - + +
629C VAL* 2.8 29.9 + - + +
631C VAL* 4.2 2.2 - - + +
637C MET* 3.5 26.7 - - - -
689C LEU* 4.2 12.6 - - + -
693C ILE* 4.0 26.7 - - + -
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Residues in contact with ARG 570 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568C ASN* 2.7 17.2 + - - +
569C LEU* 1.3 74.1 - - - +
571C GLU* 1.3 67.0 + - + +
573C LEU* 3.4 3.3 + - - +
574C GLN* 3.0 47.0 + - - +
626C ALA* 3.5 18.3 + - + +
627C ARG* 4.7 11.9 - - - +
666C TRP* 4.1 10.5 - - - -
692C GLU* 3.3 24.7 + - - +
697C GLY* 3.7 23.2 + - - +
698C GLY 3.3 18.6 + - - -
699C SER* 3.6 22.4 + - - +
700C PRO* 3.9 5.1 - - - +
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Residues in contact with GLU 571 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566C LYS 5.5 0.2 - - - +
567C GLY* 4.9 7.7 - - - -
568C ASN* 3.1 41.0 + - - +
570C ARG* 1.3 80.0 - - + +
572C TYR* 1.3 64.0 + - - +
574C GLN* 3.3 10.9 + - - +
575C ALA* 3.0 26.7 + - - +
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Residues in contact with TYR 572 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566C LYS* 4.2 15.2 + - + +
568C ASN 2.9 18.0 + - - +
569C LEU* 3.3 13.0 - - + +
571C GLU* 1.3 78.0 - - - +
573C LEU* 1.3 74.8 + - + +
575C ALA* 3.7 1.2 + - - -
576C ARG* 3.1 81.0 + - - +
595C LEU* 3.9 21.7 - - + +
603C CYS* 5.6 2.7 - - - -
631C VAL* 3.7 31.4 - - + -
635C ASN* 2.9 35.5 + - + +
637C MET* 4.4 11.2 - - + +
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Residues in contact with LEU 573 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569C LEU* 2.8 42.6 + - + +
570C ARG* 3.8 2.9 - - - +
572C TYR* 1.3 81.4 - - + +
574C GLN* 1.3 67.1 + - - +
576C ARG* 3.1 19.1 + - - +
577C ARG* 3.5 6.2 - - - +
595C LEU* 3.7 26.0 - - + +
600C LEU* 3.9 15.3 - - + -
603C CYS* 4.9 4.0 - - - -
626C ALA* 5.9 0.7 - - + -
692C GLU* 3.7 9.0 - - + +
693C ILE* 3.5 40.4 - - + +
696C LEU* 3.6 18.8 - - + +
697C GLY* 3.9 3.6 - - - +
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Residues in contact with GLN 574 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570C ARG* 3.0 32.2 + - - +
571C GLU* 3.3 9.7 + - - +
573C LEU* 1.3 72.4 - - - +
575C ALA* 1.3 55.5 + - - +
576C ARG 2.7 14.9 + - - -
577C ARG* 3.0 42.9 + - - +
696C LEU 3.5 16.4 - - - +
697C GLY* 3.3 21.1 + - - -
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Residues in contact with ALA 575 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571C GLU 3.0 13.9 + - - +
572C TYR* 4.1 4.5 - - - +
574C GLN* 1.3 77.4 - - - +
576C ARG* 1.3 68.1 + - - +
577C ARG 3.4 3.1 + - - +
593C GLU* 3.3 27.8 - - - +
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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