Contacts of the strand formed by residues 785 - 794 (chain C) in PDB entry 3N1P
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 SER 785 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160B ARG* 5.3 2.2 - - - +
184B ALA* 4.1 23.5 - - - +
754C PRO* 3.5 0.3 - - - +
755C THR* 2.6 46.8 + - - +
784C THR* 1.3 83.5 - - - +
786C TYR* 1.3 64.4 + - - +
806C ILE* 3.5 17.8 - - - +
807C CYS 3.7 6.2 + - - -
808C GLU* 3.8 17.4 + - - +
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Residues in contact with TYR 786 (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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729C ILE* 4.3 9.2 - - + -
752C TYR* 4.7 6.3 - + + -
753C ARG* 3.2 24.0 - - - -
754C PRO* 3.6 23.0 - - + +
755C THR* 3.1 6.6 + - - -
780C LEU* 3.7 45.4 - - + +
781C GLN* 3.0 31.1 + - - +
784C THR* 3.5 35.6 - - + +
785C SER* 1.3 71.7 + - - +
787C ASP* 1.3 65.0 - - - +
788C ILE* 3.7 12.0 + - + +
805C MET 3.5 0.7 - - - +
806C ILE* 3.4 3.3 - - - -
807C CYS 2.8 38.7 + - - +
809C THR* 4.5 1.1 - - + -
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Residues in contact with ASP 787 (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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92B LYS* 2.8 34.4 + - - -
94B GLU* 4.4 3.1 - - - -
752C TYR* 3.1 6.6 - - - -
753C ARG* 2.7 53.8 + - - +
755C THR* 3.1 29.0 + - - +
763C TYR* 3.6 22.5 - - + +
786C TYR* 1.3 73.0 - - - +
788C ILE* 1.3 61.0 + - - +
804C VAL* 4.3 7.6 - - + -
805C MET 3.6 4.7 - - - -
806C ILE* 3.9 8.4 - - - +
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Residues in contact with ILE 788 (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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718C ILE* 3.7 9.3 - - + +
721C THR* 5.0 8.7 - - + -
729C ILE* 4.1 37.5 - - + -
731C LEU* 4.2 25.1 - - + -
750C ILE* 4.4 10.1 - - + -
751C TYR 3.3 9.2 - - - +
752C TYR* 4.0 11.4 - - + -
777C ILE* 4.3 10.5 - - + -
780C LEU* 6.1 0.2 - - + -
786C TYR* 4.1 9.4 - - + +
787C ASP* 1.3 80.9 - - - +
789C LYS* 1.3 64.0 + - - +
804C VAL* 3.4 3.5 - - - +
805C MET* 2.7 45.1 + - + +
807C CYS* 4.4 13.2 - - + -
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Residues in contact with LYS 789 (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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94B GLU 4.2 11.3 + - - -
96B ASN* 4.4 10.7 - - - +
718C ILE* 3.9 4.3 - - - -
750C ILE* 3.7 0.7 - - - -
751C TYR* 2.7 47.9 + - + +
760C ASP* 4.7 8.5 + - - +
763C TYR* 3.5 41.9 + - + +
788C ILE* 1.3 75.9 - - - +
790C MET* 1.3 58.4 + - - +
801C PHE* 3.7 46.5 - - + -
802C SER 4.0 4.0 - - - +
803C ASN 3.8 15.5 - - - +
804C VAL* 3.8 23.1 - - + -
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Residues in contact with MET 790 (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* 3.6 20.9 - - + -
718C ILE* 3.9 10.8 - - + -
731C LEU* 4.5 5.2 - - + -
733C TRP* 3.5 52.3 - - + -
748C PHE* 3.5 31.6 - - + -
749C TYR 3.0 17.9 - - - +
750C ILE* 4.1 10.5 - - + -
751C TYR* 4.5 2.5 - - - -
789C LYS* 1.3 76.7 - - - +
791C GLN* 1.3 64.7 + - - +
801C PHE* 3.3 4.0 - - - -
802C SER* 2.6 57.3 + - - +
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Residues in contact with GLN 791 (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* 3.6 13.2 - - - -
748C PHE* 3.3 2.7 - - - +
749C TYR* 2.8 35.5 + - + +
751C TYR* 2.8 42.3 + - + -
790C MET* 1.3 78.9 - - - +
792C CYS* 1.3 60.3 + - - +
793C PHE* 4.5 0.3 - - - -
798C GLU* 3.6 25.3 - - + +
799C SER* 2.8 22.9 + - - +
800C GLU 3.4 11.4 - - - +
801C PHE* 3.4 26.3 - - - -
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Residues in contact with CYS 792 (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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712C PRO* 4.3 7.0 - - - -
714C ALA 3.7 12.8 - - - -
716C PRO* 3.5 7.6 - - + +
735C TYR* 3.8 10.3 - - - -
745C ILE* 3.6 24.9 - - + -
747C GLY 3.6 6.7 - - - +
748C PHE* 3.4 27.6 - - + -
791C GLN* 1.3 74.6 - - - +
793C PHE* 1.3 60.8 + - - +
798C GLU* 3.5 1.0 - - - +
799C SER* 2.7 55.7 + - - -
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Residues in contact with PHE 793 (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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712C PRO* 4.1 6.1 - - - -
745C ILE* 3.7 5.9 - - - +
746C HIS* 2.9 52.3 + - + -
747C GLY* 3.2 23.1 + - - +
748C PHE* 3.4 13.7 - - - -
749C TYR* 3.4 40.8 - + - -
767C MET* 3.9 22.9 - - + -
792C CYS* 1.3 80.5 - - - +
794C ASN* 1.3 73.7 + - - +
797C GLY 3.2 16.6 - - - +
798C GLU* 3.7 11.9 - - + -
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Residues in contact with ASN 794 (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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712C PRO* 3.2 32.9 - - - +
743C THR* 4.1 15.0 - - - +
744C PRO* 3.1 33.3 + - + +
746C HIS* 3.3 22.4 - - + +
793C PHE* 1.3 83.3 - - - +
795C GLU* 1.3 60.6 + - - +
796C GLY* 2.7 32.6 + - - -
797C GLY* 3.1 13.7 + - - +
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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