Contacts of the helix formed by residues 723 - 736 (chain D) in PDB entry 1V40
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 ASN 723 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3001A GOL 4.5 2.9 + - - -
698D PHE* 3.9 17.7 - - + -
718D GLU* 3.7 5.1 + - - +
719D LEU* 3.0 40.7 + - + +
722D TYR* 1.3 85.8 - - - +
724D ALA* 1.3 66.6 + - - +
725D PRO* 3.3 2.9 - - - -
726D HIS* 3.2 22.6 + - - +
727D LEU* 3.7 5.0 + - - +
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Residues in contact with ALA 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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698D PHE* 3.7 24.4 - - + -
719D LEU 2.8 13.9 + - - +
720D LEU* 3.5 19.5 - - + +
723D ASN* 1.3 71.4 - - - +
725D PRO* 1.3 69.6 - - + +
727D LEU* 3.0 7.2 + - - +
728D MET* 2.8 28.8 + - + +
760D LEU* 5.9 0.2 - - + -
767D LEU* 3.9 22.2 - - + -
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Residues in contact with PRO 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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720D LEU 3.6 7.6 - - - +
721D THR* 3.2 28.3 - - - +
722D TYR 4.0 1.1 - - - -
723D ASN 3.3 6.5 - - - +
724D ALA* 1.3 93.7 - - + +
726D HIS* 1.3 64.5 + - + +
728D MET* 3.5 8.1 + - + +
729D GLN* 3.0 28.9 + - - +
767D LEU* 6.2 0.4 - - + -
771D HIS* 4.7 5.2 - - + -
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Residues in contact with HIS 726 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3001A GOL 3.3 32.0 + - - +
722D TYR 3.2 27.0 + - - -
723D ASN* 3.2 8.5 + - - +
724D ALA 3.1 1.0 + - - -
725D PRO* 1.3 82.2 - - + +
727D LEU* 1.3 58.6 + - - +
729D GLN* 3.5 5.0 + - - +
730D ASP* 3.0 33.3 + - - +
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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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48A PHE* 4.1 10.3 - - + -
3001A GOL 3.9 10.0 + - - +
694D THR* 3.8 28.5 - - + +
695D LEU* 4.6 13.9 - - + -
698D PHE* 3.7 44.9 - - + -
723D ASN 3.7 5.6 + - - +
724D ALA* 3.0 10.2 + - - +
726D HIS* 1.3 76.0 - - - +
728D MET* 1.3 81.8 + - + +
730D ASP* 3.3 3.3 + - + +
731D LEU* 2.9 37.2 + - + +
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Residues in contact with MET 728 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698D PHE* 5.3 0.4 - - + -
724D ALA* 2.8 25.0 + - + +
725D PRO* 3.8 4.7 - - + +
727D LEU* 1.3 102.3 - - + +
729D GLN* 1.3 56.6 + - - +
731D LEU* 3.3 4.6 + - + +
732D ASP* 2.9 30.5 + - - +
753D TRP* 3.5 37.5 - - + -
760D LEU* 4.8 11.7 - - + -
767D LEU* 3.9 32.8 - - + +
768D LEU* 3.7 13.0 - - + -
771D HIS* 3.7 24.0 - - + +
774D LEU* 3.6 9.0 - - + +
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Residues in contact with GLN 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 PRO 3.0 18.3 + - - +
726D HIS* 3.8 5.6 - - - +
728D MET* 1.3 77.4 - - - +
730D ASP* 1.3 59.8 + - - +
732D ASP* 3.1 13.2 + - - +
733D THR* 2.8 54.2 + - - +
771D HIS* 3.4 21.6 + - - +
773D ARG* 5.9 0.6 - - - +
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Residues in contact with ASP 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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46A LEU 5.4 0.3 - - - +
47A PRO 3.6 16.8 - - - +
48A PHE* 3.5 29.9 - - + +
49A GLY 5.2 0.2 - - - -
3001A GOL 3.1 40.1 - - - -
726D HIS 3.0 17.5 + - - +
727D LEU* 3.6 3.8 - - - +
729D GLN* 1.3 78.7 - - - +
731D LEU* 1.3 58.2 + - - +
733D THR* 3.5 5.6 + - - -
734D TYR* 2.9 30.0 + - - +
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Residues in contact with LEU 731 (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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48A PHE* 3.6 22.2 - - + -
691D ILE* 4.7 16.6 - - + -
694D THR* 5.4 1.6 - - + -
695D LEU* 3.8 22.9 - - + -
727D LEU* 2.9 34.2 + - + +
728D MET* 3.6 7.4 - - + +
730D ASP* 1.3 74.3 - - - +
732D ASP* 1.3 59.9 + - - +
734D TYR* 3.2 3.9 + - + +
735D LEU* 2.8 31.9 + - - +
741D LEU* 4.7 12.9 - - + +
753D TRP* 3.6 37.7 - - + -
774D LEU* 4.2 13.8 - - + +
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Residues in contact with ASP 732 (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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728D MET 2.9 18.2 + - - +
729D GLN* 3.5 9.7 + - - +
731D LEU* 1.3 74.2 - - - +
733D THR* 1.3 58.3 + - - +
735D LEU* 3.2 3.4 + - - +
736D GLY 2.8 26.7 + - - +
770D ASN 4.3 1.4 - - - +
771D HIS* 2.8 43.3 - - + +
772D PRO* 5.5 0.5 - - - +
773D ARG* 2.9 49.2 + - - +
774D LEU* 4.2 11.9 - - + +
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Residues in contact with THR 733 (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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729D GLN* 2.8 36.8 + - - +
730D ASP* 3.7 6.9 - - - -
732D ASP* 1.3 75.5 - - - +
734D TYR* 1.3 65.0 + - - +
736D GLY* 3.2 12.8 + - - -
773D ARG* 4.6 4.7 - - - +
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Residues in contact with TYR 734 (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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47A PRO* 5.1 8.3 - - + +
48A PHE* 3.9 24.9 - + + -
62A HIS* 4.9 6.8 - + - -
687D HIS* 3.6 35.2 + + - +
691D ILE* 3.7 30.1 - - + +
730D ASP 2.9 19.2 + - - +
731D LEU* 3.4 5.8 - - + +
733D THR* 1.3 79.9 - - - +
735D LEU* 1.3 57.2 + - - +
738D ARG* 2.9 31.7 + - - -
741D LEU* 3.3 34.2 + - + -
742D ILE* 3.9 6.1 - - - +
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Residues in contact with LEU 735 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731D LEU 2.8 20.4 + - - +
732D ASP* 3.7 3.6 - - - +
734D TYR* 1.3 75.7 - - - +
736D GLY* 1.3 75.0 + - - +
738D ARG* 3.0 47.9 + - - +
739D GLU 4.5 0.9 - - - +
740D TRP* 3.4 35.9 - - - +
741D LEU* 3.7 15.0 - - + +
773D ARG* 3.8 29.4 - - + +
774D LEU* 4.2 15.5 - - + -
777D LEU* 4.3 14.4 - - + -
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Residues in contact with GLY 736 (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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732D ASP 2.8 15.2 + - - -
733D THR* 3.2 10.8 + - - -
734D TYR 4.6 0.2 - - - -
735D LEU* 1.3 86.7 - - - +
737D GLY* 1.3 59.5 + - - -
738D ARG* 3.4 3.6 + - - +
773D ARG* 3.2 34.5 + - - -
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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