Contacts of the helix formed by residues 718 - 729 (chain D) in PDB entry 1O23
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 718 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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713D TYR* 3.6 13.0 - - - -
717D GLY* 1.3 69.5 - - - -
719D GLU* 1.3 63.1 + - - +
720D ASP* 3.2 9.6 + - - -
721D ASP* 3.1 18.3 + - - -
722D ASP* 2.9 20.6 + - - +
761D ARG* 3.8 14.8 - - - +
762D PHE* 6.5 0.2 - - - -
765D ILE* 3.4 13.7 - - - +
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Residues in contact with GLU 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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630D ARG* 2.8 31.9 + - + +
631D ALA* 3.9 31.0 - - + +
710D PRO* 4.6 1.2 - - + +
713D TYR* 3.5 31.6 - - + +
717D GLY 3.3 12.5 + - - +
718D GLY* 1.3 71.4 - - - -
720D ASP* 1.3 63.2 + - - -
722D ASP* 3.3 5.0 - - - +
723D ILE* 2.9 34.2 + - + +
810D UPG 2.2 47.1 + - - -
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Residues in contact with ASP 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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630D ARG* 4.4 4.5 - - - +
688D TYR* 4.5 1.4 + - - -
691D TYR* 3.5 17.8 - - - -
692D PHE* 3.8 27.9 - - - +
693D GLY* 3.4 18.2 + - - -
717D GLY* 4.7 1.0 - - - -
718D GLY 3.6 17.0 + - - -
719D GLU* 1.3 80.8 - - - +
721D ASP* 1.3 71.7 + - - +
723D ILE* 3.4 10.9 + - - +
724D TYR* 2.9 26.7 + - - +
810D UPG 3.4 22.2 + - - +
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Residues in contact with ASP 721 (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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434C HIS* 5.2 2.1 - - - -
512C MET* 3.5 23.2 - - + +
688D TYR* 2.6 39.8 + - - -
690D GLN 4.4 4.1 - - - +
691D TYR* 5.0 1.0 - - - -
692D PHE 5.4 0.2 + - - -
718D GLY* 3.1 18.1 + - - +
720D ASP* 1.3 84.2 + - - +
722D ASP* 1.3 61.0 + - - +
724D TYR* 3.2 8.4 + - - +
725D ASN* 2.8 34.2 + - - +
762D PHE* 5.8 2.4 - - - -
765D ILE* 3.9 13.9 - - + +
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Residues in contact with ASP 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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710D PRO* 3.5 5.6 - - + +
713D TYR* 2.8 41.6 + - + +
718D GLY 2.9 8.8 + - - +
719D GLU* 3.3 9.6 - - - +
721D ASP* 1.3 73.8 - - - +
723D ILE* 1.3 67.4 + - - +
725D ASN* 2.8 15.3 + - - +
726D ARG* 2.7 48.4 + - - +
764D ARG 4.2 0.9 - - - +
765D ILE* 4.0 2.9 - - - +
768D THR* 2.6 33.1 + - - +
771D THR* 4.6 4.3 + - - -
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Residues in contact with ILE 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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630D ARG* 5.0 6.7 - - - +
631D ALA* 4.8 6.1 - - + -
634D LEU* 5.1 1.1 - - + -
692D PHE* 3.7 26.9 - - + -
706D ILE* 4.8 2.9 - - + -
709D PHE* 3.3 61.7 - - + -
710D PRO* 4.0 11.7 - - + -
719D GLU* 2.9 26.3 + - + +
720D ASP* 3.6 9.2 - - - +
722D ASP* 1.3 75.6 + - - +
724D TYR* 1.3 63.2 + - - +
726D ARG* 3.1 20.3 + - - +
727D LEU* 3.1 17.7 + - + +
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Residues in contact with TYR 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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515C GLU* 5.8 2.5 - - - -
516C LYS* 4.8 10.7 + - - -
689D VAL* 4.3 6.7 + - - +
690D GLN* 3.1 60.7 - - + +
691D TYR 4.8 0.9 - - - -
692D PHE* 4.2 11.6 - - + +
720D ASP 2.9 15.5 + - - +
721D ASP* 3.3 10.3 - - - +
723D ILE* 1.3 75.1 - - - +
725D ASN* 1.3 80.7 + - - +
727D LEU* 3.1 20.2 + - - +
728D ALA* 3.2 19.5 + - + +
734D VAL* 4.1 28.7 - - + -
736D ARG* 5.0 1.8 - - - -
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Residues in contact with ASN 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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721D ASP* 2.8 16.2 + - - +
722D ASP 2.8 10.1 + - - +
724D TYR* 1.3 84.7 - - - +
726D ARG* 1.3 63.0 + - - +
728D ALA* 3.0 10.4 + - - +
729D PHE* 2.9 36.0 + - + -
765D ILE* 2.7 36.2 + - - +
768D THR* 3.2 20.0 + - + -
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Residues in contact with ARG 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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706D ILE* 3.1 35.1 + - + +
707D ASN 3.6 5.1 + - - -
708D GLY 3.1 27.4 + - - -
709D PHE* 3.9 1.4 - - - +
710D PRO* 3.0 33.4 - - - +
722D ASP* 2.7 31.6 + - - +
723D ILE* 3.1 14.1 + - - +
725D ASN* 1.3 73.5 - - - +
727D LEU* 1.3 64.8 + - - +
729D PHE* 3.0 13.3 + - - +
730D ARG* 3.2 13.3 + - - +
768D THR* 3.5 12.1 - - + +
771D THR* 4.8 2.0 + - - -
772D MET* 3.5 40.3 + - + +
775D ASP* 2.8 31.3 + - - +
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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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672D PRO* 3.5 34.5 - - + -
692D PHE* 3.7 39.0 - - + -
698D LEU* 4.1 19.5 - - + -
706D ILE* 4.1 10.5 - - + -
723D ILE* 3.1 13.7 + - + +
724D TYR* 3.1 9.8 + - - +
726D ARG* 1.3 75.0 - - - +
728D ALA* 1.3 63.7 + - - +
730D ARG* 3.0 11.4 + - - -
732D MET* 3.2 42.3 + - + +
734D VAL* 4.0 14.8 - - + -
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Residues in contact with ALA 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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724D TYR* 3.2 19.8 + - + +
725D ASN* 3.0 12.6 + - - +
727D LEU* 1.3 74.7 - - - +
729D PHE* 1.3 62.1 + - + +
730D ARG 2.8 11.1 + - - -
731D GLY* 3.1 13.0 + - - -
732D MET 3.9 9.8 + - - +
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Residues in contact with PHE 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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725D ASN* 2.9 34.6 + - + -
726D ARG 3.0 7.1 + - - +
728D ALA* 1.3 76.7 - - + +
730D ARG* 1.3 72.4 + - - +
731D GLY 3.6 1.1 - - - -
766D ALA 6.2 0.4 - - - -
768D THR* 4.0 13.7 - - + -
769D LYS* 3.2 79.6 + - + +
772D MET* 4.1 12.1 - - - -
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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