Contacts of the helix formed by residues 716 - 730 (chain D) in PDB entry 1SOJ
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 PRO 716 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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714D LYS 3.4 8.7 - - - +
715D ILE* 1.3 82.0 - - + +
717D THR* 1.3 66.1 + - - +
718D GLN* 3.3 0.7 - - + +
719D GLN* 3.1 39.9 - - + +
720D PHE* 3.3 19.8 + - - +
870D PHE* 3.5 17.9 - - - +
872D LEU* 3.8 18.2 - - + -
873D HIS* 4.8 2.5 - - + +
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Residues in contact with THR 717 (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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701D TYR* 3.6 39.3 + - + +
710D LEU* 5.3 4.6 - - - +
715D ILE* 3.4 4.9 + - - -
716D PRO* 1.3 71.2 - - - +
718D GLN* 1.3 65.0 + - - +
720D PHE* 3.3 5.1 + - - +
721D MET* 3.0 33.5 + - + +
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Residues in contact with GLN 718 (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* 3.3 1.4 - - + -
717D THR* 1.3 80.3 - - - +
719D GLN* 1.3 69.8 + - + +
721D MET* 3.2 5.6 + - - +
722D ASN* 2.7 67.2 + - - +
725D ARG* 5.6 2.8 - - - +
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Residues in contact with GLN 719 (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* 3.1 34.0 - - - +
718D GLN* 1.3 86.6 - - + +
720D PHE* 1.3 62.3 + - - +
722D ASN* 3.5 2.5 - - - +
723D TYR* 3.0 25.3 + - - +
866D PRO 4.4 2.9 - - - +
867D GLU* 3.2 33.8 - - + +
868D TYR 3.8 1.6 - - - +
869D ASN 4.0 10.8 - - - +
870D PHE* 3.9 22.7 - - + +
872D LEU* 4.9 7.4 - - - +
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Residues in contact with PHE 720 (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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697D SER 4.8 0.2 - - - -
700D MET* 4.1 12.1 - - + -
701D TYR* 3.7 35.4 - + + -
704D PHE* 3.4 45.5 - + + -
710D LEU* 4.5 4.3 - - + -
715D ILE* 3.8 11.2 - - + -
716D PRO 3.3 17.3 + - - +
717D THR* 3.4 7.2 - - - +
718D GLN 3.1 0.6 - - - -
719D GLN* 1.3 79.6 - - - +
721D MET* 1.3 78.7 + - - +
723D TYR* 3.4 0.5 + - - +
724D PHE* 3.0 62.7 + + + -
870D PHE* 3.6 25.0 - + - +
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Residues in contact with MET 721 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697D SER* 3.6 21.8 - - - +
698D GLN* 3.5 29.6 - - - +
701D TYR* 3.9 20.0 - - + -
717D THR* 3.0 28.0 + - + +
718D GLN* 3.7 5.8 - - - +
720D PHE* 1.3 93.0 - - - +
722D ASN* 1.3 69.7 + - - +
724D PHE* 3.1 2.0 + - - +
725D ARG* 2.7 64.7 + - - +
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Residues in contact with ASN 722 (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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718D GLN* 2.7 56.6 + - - +
719D GLN* 3.5 1.4 - - - +
721D MET* 1.3 74.8 - - - +
723D TYR* 1.3 60.6 + - - +
725D ARG* 3.6 10.2 + - - +
726D ALA* 3.2 16.1 + - - +
867D GLU* 3.2 42.4 + - + +
868D TYR* 3.6 17.9 - - + -
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Residues in contact with TYR 723 (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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719D GLN 3.0 16.9 + - - +
720D PHE 3.9 1.8 - - - +
722D ASN* 1.3 76.4 - - - +
724D PHE* 1.3 84.4 + + - +
726D ALA* 3.2 2.8 + - - +
727D LEU* 2.8 43.1 + - + +
820D MET* 3.3 26.2 - - + +
858D ALA 2.9 18.7 + - - -
861D LEU* 3.4 25.4 - - + -
862D TYR* 3.5 38.6 - + + -
868D TYR* 3.6 29.1 - + + +
870D PHE* 3.8 20.9 - + + -
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Residues in contact with PHE 724 (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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696D LEU* 5.2 1.9 - - + +
697D SER* 4.0 20.1 + - - -
700D MET* 3.9 31.0 - - + -
720D PHE* 3.0 66.2 + + + +
721D MET* 4.2 1.8 - - - +
723D TYR* 1.3 87.4 - + - +
725D ARG* 1.3 65.6 + - - +
727D LEU* 3.6 30.5 - - + +
728D GLU* 3.1 27.5 + - - +
816D VAL* 4.2 18.4 - - + -
819D ALA* 4.1 6.1 - - + -
870D PHE* 3.6 26.9 - + - -
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Residues in contact with ARG 725 (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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694D ARG* 3.5 55.8 - - - +
697D SER* 3.6 10.6 + - - +
698D GLN* 4.2 6.5 - - - +
718D GLN* 5.6 2.4 - - - +
721D MET* 2.7 72.9 + - - +
722D ASN* 3.6 11.2 + - - +
724D PHE* 1.3 71.4 - - - +
726D ALA* 1.3 63.5 - - - +
728D GLU* 3.2 21.1 + - - +
729D ASN* 3.2 22.1 + - - +
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Residues in contact with ALA 726 (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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722D ASN 3.2 9.8 + - - +
723D TYR 3.6 7.4 - - - +
725D ARG* 1.3 77.9 - - - +
727D LEU* 1.3 65.4 + - - +
729D ASN* 3.5 16.0 + - - +
730D GLY 3.4 13.5 + - - -
823D TYR* 4.2 3.6 + - - -
861D LEU* 4.0 16.5 - - + +
868D TYR* 3.5 28.7 - - + +
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Residues in contact with LEU 727 (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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696D LEU* 4.3 4.5 - - + -
723D TYR* 2.8 41.9 + - + +
724D PHE* 3.7 34.1 - - + +
725D ARG 3.2 0.4 - - - -
726D ALA* 1.3 78.6 - - - +
728D GLU* 1.3 63.5 + - - +
730D GLY 3.1 0.9 + - - -
731D TYR* 3.5 5.6 - - + -
819D ALA* 3.3 32.8 - - + +
820D MET* 3.9 17.0 - - + -
823D TYR* 3.1 50.7 - - + -
858D ALA* 4.0 5.4 - - + -
861D LEU* 3.9 4.5 - - + +
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Residues in contact with GLU 728 (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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693D GLY 3.5 3.9 - - - +
694D ARG* 2.9 38.3 - - - +
695D ILE 3.2 0.3 + - - -
696D LEU* 2.9 25.8 + - + -
697D SER* 2.6 40.1 + - - -
724D PHE 3.1 10.9 + - - +
725D ARG* 3.2 14.7 + - - +
727D LEU* 1.3 71.6 - - - +
729D ASN* 1.3 55.3 + - - +
730D GLY 2.9 4.7 - - - -
731D TYR* 2.7 36.0 + - - +
739D ARG* 3.2 30.5 + - + +
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Residues in contact with ASN 729 (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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693D GLY 5.0 0.9 - - - +
725D ARG* 3.2 20.6 + - - +
726D ALA* 3.7 16.2 - - - +
727D LEU 3.4 0.2 - - - -
728D GLU* 1.3 77.7 - - - +
730D GLY* 1.3 60.1 + - - +
731D TYR 3.2 6.5 + - - +
739D ARG* 3.3 18.5 + - - +
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Residues in contact with GLY 730 (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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726D ALA 3.4 3.4 + - - -
727D LEU 3.1 3.6 + - - -
728D GLU 2.8 2.2 + - - -
729D ASN* 1.3 77.1 - - - +
731D TYR* 1.3 61.4 + - - +
732D ARG* 3.4 2.6 + - - +
823D TYR* 3.2 33.4 - - - -
824D ASP* 3.2 31.4 - - - +
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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