Contacts of the helix formed by residues 715 - 731 (chain C) in PDB entry 3QHE
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 HIS 715 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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726A LEU* 6.5 0.9 - - + -
730A MET* 3.4 30.6 - - + +
674C LEU* 4.4 21.7 - - + +
675C THR* 6.0 0.6 - - - -
678C SER* 3.6 14.5 - - - -
713C SER* 3.1 13.7 + - - +
714C LYS* 1.3 75.4 - - - +
716C LYS* 1.3 58.2 + - - +
717C MET* 3.2 51.1 + - + +
718C ILE* 3.0 34.9 + - + +
719C ALA* 3.0 29.8 + - - +
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Residues in contact with LYS 716 (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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730A MET* 5.7 0.2 - - - +
714C LYS 3.3 7.3 + - - +
715C HIS* 1.3 71.6 + - - +
717C MET* 1.3 61.9 + - + +
719C ALA* 3.4 6.6 + - - +
720C MET* 3.0 48.2 + - + +
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Residues in contact with MET 717 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640C ARG* 4.0 16.2 + - - +
678C SER* 3.4 22.2 - - - +
681C CYS* 4.7 1.6 - - - +
685C TRP* 5.7 0.2 - - - -
715C HIS* 3.2 37.6 + - + +
716C LYS* 1.3 76.2 - - + +
718C ILE* 1.3 57.8 + - - +
720C MET* 3.9 11.0 - - + +
721C GLY* 2.8 33.3 + - - -
380D TYR* 3.6 47.6 - - + +
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Residues in contact with ILE 718 (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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674C LEU* 3.8 28.9 - - + +
677C VAL* 3.7 22.9 - - + -
678C SER* 3.8 20.2 - - - +
681C CYS* 4.1 10.3 - - - -
710C LEU* 4.0 28.0 - - + -
713C SER* 3.8 18.8 - - - +
715C HIS* 3.0 38.4 + - + +
717C MET* 1.3 72.2 - - - +
719C ALA* 1.3 59.2 + - - +
722C SER* 2.8 37.6 + - - -
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Residues in contact with ALA 719 (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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710C LEU 3.9 4.0 - - - -
711C ILE* 3.5 22.8 - - - +
713C SER* 3.7 14.7 - - - +
715C HIS 3.0 18.2 + - - +
716C LYS* 3.6 6.5 - - - +
718C ILE* 1.3 75.1 - - - +
720C MET* 1.3 57.5 + - - +
722C SER* 2.9 7.8 + - - -
723C ALA* 2.9 32.7 + - - +
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Residues in contact with MET 720 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685C TRP* 3.7 33.7 - - + -
716C LYS* 3.0 31.9 + - + +
717C MET* 4.0 11.2 - - + +
719C ALA* 1.3 77.4 - - - +
721C GLY* 1.3 56.8 + - - +
723C ALA* 3.4 5.0 + - - +
724C ALA* 2.8 34.4 + - + +
727C ARG* 5.0 2.5 + - - +
380D TYR* 4.6 14.8 - - - +
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Residues in contact with GLY 721 (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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681C CYS* 3.8 22.8 - - - +
682C GLY* 5.0 0.4 - - - -
685C TRP* 3.8 21.7 - - - +
717C MET 2.8 22.3 + - - -
718C ILE 3.9 0.2 - - - -
720C MET* 1.3 70.1 - - - +
722C SER* 1.3 63.2 + - - +
724C ALA* 4.1 1.0 - - - +
725C ALA* 3.1 25.5 + - - +
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Residues in contact with SER 722 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681C CYS* 3.8 11.8 - - - +
707C LEU* 3.6 36.1 - - - +
710C LEU* 3.3 11.7 + - - -
711C ILE* 3.3 20.9 + - - -
718C ILE 2.8 25.9 + - - -
719C ALA 2.9 10.4 + - - -
721C GLY* 1.3 72.5 - - - +
723C ALA* 1.3 61.7 + - - +
725C ALA* 3.4 1.9 + - - +
726C LEU* 3.0 26.0 + - - +
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Residues in contact with ALA 723 (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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711C ILE* 3.7 20.4 - - + +
719C ALA 2.9 20.1 + - - +
720C MET* 3.8 5.4 - - - +
722C SER* 1.3 77.5 + - - +
724C ALA* 1.3 57.1 + - - +
726C LEU* 3.3 5.6 + - - +
727C ARG* 3.0 45.5 + - - +
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Residues in contact with ALA 724 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685C TRP* 3.5 41.1 - - + +
720C MET* 2.8 22.3 + - + +
721C GLY 4.2 0.2 - - - +
723C ALA* 1.3 70.6 - - - +
725C ALA* 1.3 61.6 + - - +
727C ARG* 3.5 20.4 + - - +
728C ASN* 3.1 34.6 + - - +
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Residues in contact with ALA 725 (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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681C CYS 4.9 0.2 - - - +
684C LEU* 4.0 8.1 - - + +
685C TRP* 3.9 16.9 - - - +
688C SER* 3.5 23.3 + - - +
707C LEU* 4.0 17.5 - - + -
721C GLY 3.1 19.0 + - - +
722C SER 3.8 3.1 - - - +
724C ALA* 1.3 73.2 - - - +
726C LEU* 1.3 66.1 + - - +
728C ASN* 3.4 4.0 + - - +
729C LEU* 3.1 28.9 + - - +
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Residues in contact with LEU 726 (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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704C VAL* 3.9 35.4 - - + +
707C LEU* 3.8 17.4 - - + +
708C LYS* 3.9 28.9 - - + +
711C ILE* 3.9 23.3 - - + -
722C SER 3.0 7.8 + - - +
723C ALA* 3.4 9.4 - - - +
725C ALA* 1.3 74.1 - - - +
727C ARG* 1.3 65.2 + - - +
729C LEU* 3.0 6.7 + - + +
730C MET* 3.0 48.7 + - + +
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Residues in contact with ARG 727 (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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720C MET* 5.0 2.8 + - - +
723C ALA* 3.0 26.1 + - - +
724C ALA* 3.7 31.4 - - - +
725C ALA 3.4 0.2 - - - -
726C LEU* 1.3 74.7 - - - +
728C ASN* 1.3 65.2 + - - +
730C MET* 3.2 22.4 + - + +
731C ALA 3.6 4.5 + - - +
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Residues in contact with ASN 728 (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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685C TRP* 3.2 34.1 + - - +
688C SER* 3.4 26.6 - - - +
689C ALA* 3.7 15.5 - - - +
694C ASP* 4.3 9.0 - - - +
724C ALA 3.1 18.6 + - - +
725C ALA 3.5 9.4 - - - +
726C LEU 3.2 0.2 - - - -
727C ARG* 1.3 78.7 - - - +
729C LEU* 1.3 61.1 + - - +
731C ALA* 3.4 14.6 + - - +
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Residues in contact with LEU 729 (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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688C SER* 4.3 13.7 - - - +
694C ASP* 3.8 39.8 - - - +
697C ALA* 4.0 12.6 - - + -
698C LEU* 4.8 18.1 - - + +
703C ALA* 4.1 13.5 - - + -
704C VAL* 3.9 28.7 - - + -
707C LEU* 3.9 23.8 - - + -
725C ALA 3.1 18.7 + - - +
726C LEU* 3.0 8.5 + - - +
728C ASN* 1.3 71.0 - - - +
730C MET* 1.3 63.0 + - + +
731C ALA* 3.1 15.3 + - - +
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Residues in contact with MET 730 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704C VAL* 4.3 19.1 - - + -
708C LYS* 6.4 1.1 - - + -
726C LEU* 3.0 44.7 + - + +
727C ARG* 3.2 14.8 + - + +
729C LEU* 1.3 78.0 - - - +
731C ALA* 1.3 68.4 + - - +
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Residues in contact with ALA 731 (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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694C ASP* 5.2 8.3 - - - +
727C ARG 3.6 4.8 + - - -
728C ASN 3.4 12.0 + - - +
729C LEU* 3.1 12.6 - - - +
730C MET* 1.3 83.8 - - - +
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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