Contacts of the helix formed by residues 710 - 723 (chain C) in PDB entry 1P93
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 GLN 710 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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708C SER 3.2 8.1 + - - +
709C SER* 1.3 98.5 + - - +
711C ASN* 1.3 55.7 + - - +
712C TRP* 2.6 25.1 + - + +
713C GLN* 2.8 33.9 + - + +
714C ARG* 4.5 5.2 + - - +
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Residues in contact with ASN 711 (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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701C ILE* 3.6 19.8 + - + +
702C VAL* 3.2 39.0 - - + +
704C ARG 4.2 1.2 + - - -
708C SER* 3.2 19.8 + - - +
709C SER 3.1 28.0 + - - +
710C GLN* 1.3 75.9 + - - +
712C TRP* 1.3 53.9 + - + +
714C ARG* 3.0 8.2 + - - +
715C PHE* 2.7 36.2 + - + +
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Residues in contact with TRP 712 (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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709C SER 5.7 1.8 - - - -
710C GLN* 2.6 12.0 + - + +
711C ASN* 1.3 79.1 - - + +
713C GLN* 1.3 52.2 + - - +
715C PHE* 3.2 43.2 - + + +
716C TYR* 2.7 36.4 + - + +
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Residues in contact with GLN 713 (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 GLN* 2.8 33.6 + - + +
712C TRP* 1.3 70.7 - - - +
714C ARG* 1.3 65.9 + - - +
716C TYR* 3.0 9.6 + - + +
717C GLN* 2.8 48.8 + - + +
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Residues in contact with ARG 714 (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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656C LEU* 2.8 33.9 + - - +
657C GLN* 3.9 4.4 + - - +
658C VAL* 3.3 7.9 - - - +
662C GLU* 2.7 33.9 + - - -
701C ILE* 3.4 25.4 - - + -
704C ARG* 2.8 33.0 - - - +
710C GLN* 3.9 5.2 + - - +
711C ASN* 3.0 13.6 + - - +
713C GLN* 1.3 79.0 - - - +
715C PHE* 1.3 64.9 + - - +
717C GLN* 3.1 22.7 + - - +
718C LEU* 3.1 46.5 + - + +
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Residues in contact with PHE 715 (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 ILE* 4.7 28.3 - - + -
697C LEU* 5.0 10.5 - - + -
698C GLY* 4.9 9.4 - - - -
701C ILE* 3.4 29.4 - - + -
711C ASN* 2.7 17.4 + - + +
712C TRP* 3.2 45.3 - + + +
714C ARG* 1.3 75.3 - - - +
716C TYR* 1.3 58.7 + - - +
718C LEU* 3.3 3.2 + - - +
719C THR* 2.5 49.2 + - + -
774C PHE* 6.4 0.2 - + - -
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Residues in contact with TYR 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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712C TRP* 2.7 18.2 + - + +
713C GLN* 3.0 12.5 + - + +
715C PHE* 1.3 76.9 - - + +
717C GLN* 1.3 81.0 + - + +
719C THR* 3.0 15.7 + - - -
720C LYS* 3.3 34.0 + - + +
775C HIS* 3.9 29.5 + + - -
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Residues in contact with GLN 717 (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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655C ARG* 5.7 3.2 - - - +
656C LEU* 4.0 29.5 - - + +
713C GLN* 2.8 35.9 + - + +
714C ARG* 3.1 32.3 + - - +
716C TYR* 1.3 92.8 - - + +
718C LEU* 1.3 62.7 + - + +
719C THR 3.3 0.2 + - - -
720C LYS* 3.4 12.0 + - - +
721C LEU* 3.8 8.7 + - - +
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Residues in contact with LEU 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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656C LEU* 4.3 22.9 - - + -
658C VAL* 4.6 9.4 - - + -
662C GLU* 3.9 23.1 - - + +
666C MET* 4.3 19.7 - - + +
697C LEU* 4.9 9.4 - - + -
701C ILE* 4.1 18.8 - - + -
714C ARG* 3.1 46.1 + - - +
715C PHE 3.8 6.1 - - - +
717C GLN* 1.3 78.5 - - - +
719C THR* 1.3 58.3 + - - +
721C LEU* 3.1 27.9 + - + +
722C LEU* 3.6 12.3 + - - +
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Residues in contact with THR 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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697C LEU* 6.2 4.7 - - + -
715C PHE* 2.5 47.1 + - + -
716C TYR* 3.0 7.3 + - - -
718C LEU* 1.3 72.0 - - - +
720C LYS* 1.3 51.3 + - - +
721C LEU 2.6 14.6 + - - -
722C LEU* 2.9 18.5 + - + +
723C ASP* 2.3 23.2 + - - +
774C PHE* 3.2 46.7 - - + -
775C HIS* 3.5 12.4 + - + +
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Residues in contact with LYS 720 (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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716C TYR* 3.3 33.0 + - + +
717C GLN 3.4 10.0 + - - +
719C THR* 1.3 75.8 - - - +
721C LEU* 1.3 56.5 + - - +
723C ASP* 3.3 31.4 - - - +
724C SER* 3.7 13.2 + - - -
773C LEU* 4.9 0.6 - - - +
775C HIS* 3.5 46.6 + - + +
776C GLN 5.9 0.7 - - - -
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Residues in contact with LEU 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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606C PHE* 5.5 4.9 - - + -
648C TYR* 3.5 34.5 - - + +
649C VAL* 5.8 5.6 - - + +
652C GLU* 4.4 28.5 - - + +
653C LEU* 4.7 16.8 - - + -
656C LEU* 5.3 7.4 - - + -
658C VAL* 5.9 0.7 - - + -
666C MET* 5.0 8.3 - - + -
717C GLN 3.8 5.6 + - - +
718C LEU* 3.1 21.7 + - + +
719C THR 2.6 6.3 + - - -
720C LYS* 1.3 74.0 - - - +
722C LEU* 1.3 63.8 + - + +
723C ASP 3.1 2.0 - - - -
724C SER* 2.8 25.0 + - - -
725C MET* 3.4 14.6 + - - +
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Residues in contact with LEU 722 (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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606C PHE* 4.2 8.5 - - + -
666C MET* 3.3 40.6 - - + -
669C LEU* 3.8 34.5 - - + -
670C LEU* 3.5 35.3 - - + +
673C SER* 4.1 7.3 + - - +
697C LEU* 5.1 2.9 - - + -
718C LEU 3.9 9.4 - - - +
719C THR* 2.9 12.1 + - + +
721C LEU* 1.3 79.9 - - + +
723C ASP* 1.3 59.6 + - - +
724C SER 3.1 1.1 - - - -
725C MET* 3.4 19.2 + - + +
726C HIS* 4.3 4.9 + - - -
774C PHE* 4.1 21.3 - - + -
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Residues in contact with ASP 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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719C THR 2.3 34.5 - - - +
720C LYS* 3.3 18.8 - - - +
722C LEU* 1.3 75.2 - - - +
724C SER* 1.3 62.0 + - - +
725C MET 3.2 0.9 - - - -
726C HIS* 3.4 27.9 + - - +
727C GLU* 4.2 7.6 + - - +
772C LEU 5.2 0.2 - - - -
773C LEU* 2.9 27.4 - - + +
774C PHE* 2.6 39.9 + - - +
775C HIS* 3.6 8.8 - - - -
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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