Contacts of the strand formed by residues 747 - 754 (chain C) in PDB entry 3N1G
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 GLY 747 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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745C ILE* 3.1 18.7 - - - +
746C HIS* 1.3 81.1 - - - +
748C PHE* 1.3 63.6 + - - -
767C MET* 5.2 0.2 - - - -
768C VAL 3.0 13.9 - - - -
770C GLY* 3.5 13.5 - - - -
792C CYS* 3.5 1.4 - - - -
793C PHE* 3.3 26.6 + - - -
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Residues in contact with PHE 748 (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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716C PRO* 3.8 19.1 - - + -
733C TRP* 3.4 24.5 - + - -
735C TYR* 4.1 25.1 - + + -
745C ILE* 4.5 5.8 - - + -
747C GLY* 1.3 72.6 - - - -
749C TYR* 1.3 61.4 + - - +
750C ILE* 4.0 1.1 - - + +
767C MET* 3.5 5.2 - - - -
768C VAL* 2.9 38.7 + - + +
769C GLU 3.7 12.1 - - - -
770C GLY* 3.6 23.1 - - - -
772C LYS 3.3 22.0 - - - -
790C MET* 3.5 17.5 - - + -
791C GLN 3.2 7.2 - - - +
792C CYS* 3.4 31.2 - - + -
793C PHE* 3.8 5.8 - - - -
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Residues in contact with TYR 749 (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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748C PHE* 1.3 73.2 - - - +
750C ILE* 1.3 61.7 + - - +
751C TYR* 3.5 31.5 - - + -
765C LYS* 3.7 34.4 + - + -
766C ASP 3.3 13.0 - - - -
767C MET* 4.0 14.4 - - + -
790C MET* 3.0 7.6 - - - +
791C GLN* 2.8 37.8 + - + -
793C PHE* 3.4 49.8 - + - -
798C GLU* 4.0 27.8 + - + -
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Residues in contact with ILE 750 (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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731C LEU* 4.0 28.3 - - + -
733C TRP* 4.2 5.8 - - + -
748C PHE* 4.0 9.9 - - + +
749C TYR* 1.3 77.3 - - - +
751C TYR* 1.3 61.2 + - - +
752C TYR* 3.7 4.5 - - - -
765C LYS* 3.5 1.7 - - - -
766C ASP* 2.8 42.0 + - + +
768C VAL* 3.7 39.0 - - + -
775C HIS* 4.5 5.6 - - + -
777C ILE* 3.7 34.1 - - + -
788C ILE* 4.2 7.6 - - + -
789C LYS 3.8 3.1 - - - +
790C MET* 4.0 12.8 - - + -
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Residues in contact with TYR 751 (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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749C TYR* 3.5 24.7 - - + -
750C ILE* 1.3 73.3 - - - +
752C TYR* 1.3 62.5 + - - +
763C TYR* 3.6 31.6 - + + -
764C LYS 3.1 7.0 - - - +
765C LYS* 3.4 36.1 + - + +
788C ILE* 3.4 7.6 - - - +
789C LYS* 2.7 46.6 + - + +
790C MET* 4.2 1.6 - - - -
791C GLN* 2.6 37.0 + - + -
798C GLU* 5.0 0.3 - - - +
801C PHE* 3.5 26.6 - + - -
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Residues in contact with TYR 752 (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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750C ILE 3.7 9.6 - - - -
751C TYR* 1.3 79.4 - - - +
753C ARG* 1.3 61.8 + - - +
754C PRO* 4.8 0.9 - - - +
762C ASP 4.1 0.5 - - - +
763C TYR* 3.6 2.7 - - - -
764C LYS* 2.8 70.2 + - + +
765C LYS 4.8 0.3 + - - -
766C ASP* 2.8 36.7 + - - -
777C ILE* 3.5 48.2 - - + +
778C SER 5.0 4.2 + - - -
780C LEU* 3.9 19.1 - - + -
786C TYR* 4.6 11.9 - + + -
787C ASP 3.2 10.1 - - - +
788C ILE* 4.2 5.8 - - + -
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Residues in contact with ARG 753 (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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88B LYS* 3.7 5.5 - - - +
90B GLU* 3.3 20.2 - - - +
752C TYR* 1.3 76.9 - - - +
754C PRO* 1.3 82.8 - - + +
757C SER* 3.1 20.2 + - - -
758C ASP* 3.4 5.2 + - - +
759C ASN 2.9 37.4 + - - +
760C ASP* 2.8 27.7 + - - +
762C ASP* 3.8 17.3 - - + +
763C TYR* 3.3 36.1 + - + -
786C TYR* 3.2 6.6 - - - -
787C ASP* 2.8 57.5 + - - +
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Residues in contact with PRO 754 (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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752C TYR 4.8 1.1 - - - +
753C ARG* 1.3 101.0 - - + +
755C THR* 1.3 59.9 + - - +
756C ASP* 4.5 8.1 - - + +
757C SER* 3.1 25.2 + - - +
762C ASP* 4.4 7.4 - - + +
764C LYS* 6.6 0.2 - - - -
784C THR* 4.8 8.3 - - + -
785C SER 3.5 9.4 - - - +
786C TYR* 3.8 20.4 - - + +
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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