Contacts of the strand formed by residues 747 - 754 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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745D ILE* 3.4 4.6 - - - +
746D HIS* 1.3 82.1 - - - +
748D PHE* 1.3 64.7 + - - -
768D VAL 3.2 13.0 - - - -
770D GLY* 3.5 14.4 - - - -
792D CYS* 3.4 7.4 - - - +
793D PHE* 3.0 35.3 + - - +
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Residues in contact with PHE 748 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716D PRO* 3.6 27.8 - - + -
733D TRP* 3.5 30.5 - + - -
735D TYR* 3.9 22.4 - + + -
745D ILE* 3.6 13.0 - - + -
747D GLY* 1.3 74.3 - - - -
749D TYR* 1.3 62.1 + - - +
750D ILE* 4.1 1.6 - - + -
766D ASP 3.8 0.3 - - - +
767D MET* 3.5 4.7 - - - -
768D VAL* 2.8 38.8 + - + +
769D GLU 3.6 12.6 - - - -
770D GLY* 3.7 22.0 - - - -
772D LYS 3.6 12.1 - - - -
790D MET* 3.7 16.6 - - + -
791D GLN 3.2 6.5 - - - +
792D CYS* 3.7 22.4 - - + -
793D PHE* 3.8 5.9 - - - -
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Residues in contact with TYR 749 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748D PHE* 1.3 78.4 - - - +
750D ILE* 1.3 62.2 + - - +
751D TYR* 3.6 21.5 - - + -
765D LYS* 3.4 35.7 + - + -
766D ASP 3.4 1.8 - - - -
767D MET* 3.9 18.4 - - + -
790D MET* 3.1 7.8 - - - +
791D GLN* 2.9 51.5 + - + -
793D PHE* 3.5 49.2 - + - -
798D GLU* 3.8 21.7 + - + -
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Residues in contact with ILE 750 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731D LEU* 4.3 14.6 - - + -
733D TRP* 4.2 8.7 - - + -
748D PHE* 4.4 0.7 - - + -
749D TYR* 1.3 76.2 - - - +
751D TYR* 1.3 65.6 + - - +
752D TYR* 3.8 4.0 - - + -
764D LYS 3.8 0.2 - - - +
765D LYS* 3.2 3.0 - - - -
766D ASP* 2.8 41.2 + - + +
768D VAL* 3.8 40.2 - - + -
775D HIS* 4.0 15.5 - - + -
777D ILE* 3.8 34.1 - - + -
788D ILE* 4.4 7.4 - - + -
789D LYS 3.7 5.4 - - - +
790D MET* 4.1 19.5 - - + -
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Residues in contact with TYR 751 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749D TYR* 3.6 20.8 - - + -
750D ILE* 1.3 74.7 - - - +
752D TYR* 1.3 63.8 + - - +
763D TYR* 3.5 30.3 - + + -
764D LYS 3.1 12.6 - - - +
765D LYS* 3.8 31.3 + - + +
788D ILE* 3.4 6.4 - - - +
789D LYS* 2.7 47.2 + - + +
790D MET* 4.2 1.3 - - - -
791D GLN* 2.4 39.2 + - + -
798D GLU* 4.8 1.0 + - - +
801D PHE* 3.5 28.5 - + - -
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Residues in contact with TYR 752 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750D ILE 3.8 6.7 - - - -
751D TYR* 1.3 79.0 - - - +
753D ARG* 1.3 63.4 + - - +
754D PRO* 4.8 1.0 - - + +
762D ASP 4.0 0.3 - - - +
763D TYR* 3.5 2.1 - - - -
764D LYS* 2.8 71.9 + - + +
765D LYS 5.0 0.2 + - - -
766D ASP* 3.4 28.8 + - - -
777D ILE* 3.3 52.2 - - + +
778D SER 4.6 6.0 + - - -
780D LEU* 3.8 20.0 - - + -
786D TYR* 4.6 11.0 - + + -
787D ASP 3.1 9.9 - - - +
788D ILE* 4.4 4.0 - - + -
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Residues in contact with ARG 753 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LYS* 3.5 7.1 + - - +
90A GLU* 3.4 26.3 - - - +
752D TYR* 1.3 76.3 - - - +
754D PRO* 1.3 84.0 - - + +
757D SER* 3.1 20.7 + - - -
758D ASP* 3.2 11.7 + - - +
759D ASN 3.1 32.5 + - - -
760D ASP* 2.9 26.5 + - - +
762D ASP* 3.8 12.8 - - + +
763D TYR* 3.4 32.4 + - + -
786D TYR* 3.3 7.0 - - - -
787D ASP* 2.7 55.5 + - - +
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Residues in contact with PRO 754 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B TYR* 3.5 36.3 - - + +
752D TYR* 4.8 0.7 - - + +
753D ARG* 1.3 97.8 - - + +
755D THR* 1.3 59.2 + - - +
756D ASP* 4.3 5.6 - - + +
757D SER* 2.9 22.7 + - - +
762D ASP* 4.5 8.7 - - + +
764D LYS* 6.5 0.4 - - + -
784D THR* 4.9 8.3 - - + -
785D SER 3.6 9.6 - - - +
786D TYR* 3.9 19.7 - - + +
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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