Contacts of the helix formed by residues 812 - 823 (chain A) in PDB entry 3T1N
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 812 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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797A ILE* 3.8 10.0 - - - +
811A LEU* 1.3 75.8 - - - +
813A GLU* 1.3 67.8 + - - +
814A LYS* 3.9 7.2 + - - +
815A TRP* 3.3 18.4 + - - +
831A TYR* 2.9 37.8 + - - +
832A LEU 5.2 0.7 - - - -
833A LEU* 3.7 24.4 - - - +
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Residues in contact with GLU 813 (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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768A SER* 3.3 12.5 - - - -
769A SER* 3.0 42.4 + - - +
770A PRO* 4.4 5.4 - - + -
775A LEU* 3.6 27.6 - - + -
797A ILE* 4.0 16.1 - - + +
798A GLY* 3.9 10.4 - - - -
799A PRO* 3.5 9.5 - - - +
812A SER* 1.3 72.4 - - - +
814A LYS* 1.3 59.1 + - + +
815A TRP 3.0 4.9 - - - -
816A VAL* 2.8 24.4 + - - +
817A LEU* 3.1 15.7 + - + +
833A LEU* 4.5 4.2 - - - +
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Residues in contact with LYS 814 (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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693A ARG* 3.8 18.4 - - - +
812A SER* 3.3 8.3 + - - +
813A GLU* 1.3 78.7 + - + +
815A TRP* 1.3 56.2 + - - +
816A VAL 3.3 0.2 - - - -
817A LEU* 3.7 12.1 - - + -
818A ASP* 2.8 49.3 + - - +
831A TYR* 3.8 8.1 - - + -
824C PHE* 4.2 17.8 + - - +
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Residues in contact with TRP 815 (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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756A PHE* 4.8 9.2 - + - -
759A GLN* 4.2 11.0 - - - -
762A MET* 4.2 28.3 - - + -
795A ILE* 4.1 21.8 - - + -
797A ILE* 4.0 8.5 - - + -
811A LEU* 3.7 25.8 - - + -
812A SER 3.3 12.7 + - - +
813A GLU 2.9 0.6 + - - -
814A LYS* 1.3 79.2 - - - +
816A VAL* 1.3 78.8 + - + +
818A ASP* 4.4 0.5 - - - +
819A SER* 2.7 37.9 + - - -
825A VAL* 4.1 18.8 - - + -
826A CYS* 3.2 22.1 + - + -
827A ALA 4.0 2.7 - - - -
828A PRO* 3.7 19.7 - - + +
831A TYR* 3.5 50.1 - + + -
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Residues in contact with VAL 816 (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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756A PHE* 3.9 14.5 - - + -
762A MET* 5.0 2.5 - - - -
764A VAL* 6.6 0.2 - - + -
775A LEU* 3.8 23.3 - - + -
778A LEU* 5.0 0.4 - - + -
779A VAL* 4.0 24.9 - - + -
797A ILE* 4.3 24.0 - - + -
813A GLU 2.8 10.7 + - - +
815A TRP* 1.3 97.2 - - + +
817A LEU* 1.3 64.0 + - - +
819A SER* 3.4 3.1 + - - -
820A ILE* 3.1 45.8 + - + +
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Residues in contact with LEU 817 (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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693A ARG* 3.7 16.6 - - - +
698A LEU* 4.0 18.5 - - + +
770A PRO* 4.3 18.6 - - + -
775A LEU* 4.3 11.9 - - + -
778A LEU* 4.0 27.1 - - + -
813A GLU* 3.1 15.8 + - + +
814A LYS* 4.1 12.1 - - + -
816A VAL* 1.3 78.8 - - + +
818A ASP* 1.3 57.3 + - - +
820A ILE* 3.3 8.1 + - + +
821A THR* 3.0 30.7 + - - -
824C PHE* 3.3 37.2 - - + +
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Residues in contact with ASP 818 (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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693A ARG* 2.9 30.1 + - - +
814A LYS* 2.8 41.0 + - - +
815A TRP 4.4 0.4 - - - +
817A LEU* 1.3 70.0 - - - +
819A SER* 1.3 60.8 + - - +
821A THR* 3.4 1.6 + - - -
822A GLN* 3.0 36.5 + - + +
826A CYS* 3.9 7.4 - - - -
831A TYR* 3.0 35.6 + - + +
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Residues in contact with SER 819 (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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755A LEU* 3.6 6.8 - - - +
756A PHE* 3.7 23.7 - - - -
815A TRP* 2.7 28.3 + - - -
816A VAL 3.7 4.7 - - - -
817A LEU 3.3 0.2 - - - -
818A ASP* 1.3 75.8 - - - +
820A ILE* 1.3 58.5 + - - +
823A HIS* 3.0 22.5 + - - -
824A LYS 3.1 24.3 + - - -
825A VAL* 3.8 3.1 - - - -
826A CYS* 3.1 24.0 + - - +
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Residues in contact with ILE 820 (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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698A LEU* 4.3 16.8 - - + +
701A ILE* 3.6 26.4 - - + +
702A ALA* 5.0 1.1 - - - +
736A ALA* 3.0 21.3 - - - +
755A LEU* 4.1 6.2 - - + +
756A PHE* 4.2 8.5 - - + -
778A LEU* 4.1 29.8 - - + -
782A CYS* 3.9 27.4 - - - -
816A VAL* 3.1 35.7 + - + +
817A LEU* 3.5 11.2 - - + +
819A SER* 1.3 77.9 - - - +
821A THR* 1.3 57.8 + - - +
823A HIS* 3.6 4.3 + - - -
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Residues in contact with THR 821 (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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693A ARG* 3.0 38.2 + - - +
698A LEU* 4.0 6.6 - - - +
701A ILE* 4.8 7.0 - - + +
733A HIS 4.5 4.5 - - - +
734A PHE* 4.3 18.8 - - + -
735A PRO* 3.6 14.9 - - + +
736A ALA* 3.0 25.3 + - - +
817A LEU 3.0 10.0 + - - -
818A ASP* 3.9 3.6 - - - -
820A ILE* 1.3 77.6 - - - +
822A GLN* 1.3 72.1 + - - +
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Residues in contact with GLN 822 (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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735A PRO* 3.5 34.4 - - - +
736A ALA* 4.2 1.8 - - - -
739A LEU* 4.8 2.3 - - - +
818A ASP* 3.0 22.3 + - + +
821A THR* 1.3 88.4 + - - +
823A HIS* 1.3 72.4 + - - +
824A LYS* 3.6 19.6 - - + +
826A CYS* 4.9 7.6 - - - -
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Residues in contact with HIS 823 (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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736A ALA* 3.8 8.1 + - + +
739A LEU* 3.3 39.5 - - + +
740A CYS* 3.4 30.1 - - - -
743A GLU* 3.5 25.0 + - - -
751A TYR* 5.3 0.2 - - - -
754A THR* 6.1 4.4 - - + +
755A LEU* 4.2 24.6 - - + +
819A SER 3.0 9.5 + - - -
820A ILE 3.6 3.7 + - - -
821A THR 3.4 2.6 - - - -
822A GLN* 1.3 81.1 - - - +
824A LYS* 1.3 59.9 + - - +
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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