Contacts of the helix formed by residues 712 - 721 (chain C) in PDB entry 3JW0
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 ILE 712 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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666C SER* 3.6 29.6 - - - -
672C THR* 3.8 10.8 - - - +
673C LEU 3.0 10.4 + - - +
674C GLN* 3.7 26.9 - - + +
711C PHE* 1.3 75.0 - - - +
713C ARG* 1.3 67.5 + - - +
714C PRO* 3.7 15.9 - - + -
715C PHE* 2.9 28.1 + - + +
716C TYR* 4.0 1.8 + - - -
732C VAL* 3.8 17.0 - - + -
796C PHE* 3.7 31.9 - - + -
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Residues in contact with ARG 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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711C PHE 3.6 2.4 + - - -
712C ILE* 1.3 69.5 - - - +
714C PRO* 1.3 73.3 - - + +
715C PHE 2.9 2.1 + - - -
716C TYR* 2.9 25.3 + - + +
717C LYS* 3.0 29.7 + - + +
727C ASN* 5.2 5.3 + - - +
728C ASP* 3.5 26.9 + - - +
731C SER* 4.0 23.5 + - - +
825C GLU* 3.0 49.4 + - + +
826C ASN* 5.9 5.2 - - - +
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Residues in contact with PRO 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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712C ILE* 3.3 25.8 - - + -
713C ARG* 1.3 94.9 - - + +
715C PHE* 1.3 57.0 + - - +
717C LYS* 3.2 4.0 + - + +
718C MET* 2.8 43.6 + - + +
724C ILE* 3.7 21.1 - - + -
728C ASP* 4.2 28.3 - - + +
732C VAL* 4.3 2.0 - - + -
796C PHE* 4.2 24.9 - - + -
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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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663C PHE* 4.3 9.0 - + - -
673C LEU 5.5 0.2 - - - +
674C GLN* 5.8 1.6 - - - -
675C ILE* 4.2 24.2 - - + -
711C PHE* 3.5 52.3 - + + -
712C ILE* 2.9 22.7 + - + +
713C ARG 2.9 3.8 + - - -
714C PRO* 1.3 71.8 - - - +
716C TYR* 1.3 71.8 + + - +
718C MET* 3.0 18.9 + - - +
719C MET* 3.3 19.3 + - - +
804C MET* 3.4 26.9 - - - +
807C PHE* 3.4 46.0 - + - -
832C MET* 4.9 2.9 - - + -
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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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710C PHE* 3.9 0.9 - - - -
711C PHE* 3.1 58.2 + + + -
712C ILE 4.1 3.8 - - - -
713C ARG* 2.9 18.2 + - + +
715C PHE* 1.3 79.8 - + - +
717C LYS* 1.3 64.3 + - - +
719C MET* 2.9 25.4 + - - +
720C LEU* 3.1 16.1 + - - +
825C GLU* 4.2 22.9 - - + +
828C LEU* 4.1 22.6 - - + +
829C GLU* 3.6 47.6 + - + -
832C MET* 4.5 10.3 - - + -
833C CYS* 3.4 18.5 - - - +
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Residues in contact with LYS 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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713C ARG* 3.0 43.6 + - + +
714C PRO 3.5 7.6 - - - +
716C TYR* 1.3 78.3 - - - +
718C MET* 1.3 58.2 + - - +
720C LEU* 3.5 6.1 + - - -
721C GLY 3.2 2.8 + - - -
722C LYS* 2.8 51.2 + - + +
723C GLN 3.3 20.1 + - - -
724C ILE* 3.8 10.3 - - + -
725C THR* 4.6 2.4 + - - -
728C ASP* 2.7 46.2 + - - +
825C GLU* 4.0 19.9 + - + +
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Residues in contact with MET 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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675C ILE* 6.4 0.2 - - - -
714C PRO* 2.8 37.7 + - + +
715C PHE* 3.0 11.4 + - - +
717C LYS* 1.3 71.1 - - - +
719C MET* 1.3 67.4 + - - +
721C GLY* 3.2 11.4 + - - -
722C LYS 4.6 6.1 - - - +
724C ILE* 3.5 29.4 - - + -
796C PHE 4.0 17.9 - - - +
797C VAL* 4.3 3.4 - - + -
800C VAL* 5.2 2.7 - - - -
801C GLN* 3.7 30.1 - - - +
804C MET* 3.9 33.0 - - + +
808C LEU* 4.7 6.4 - - - +
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Residues in contact with MET 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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715C PHE* 3.7 18.8 - - + +
716C TYR* 2.9 11.5 + - - +
718C MET* 1.3 74.4 - - - +
720C LEU* 1.3 59.4 + - + +
721C GLY* 2.9 10.7 + - - -
804C MET* 3.9 16.8 - - + -
807C PHE* 4.1 13.9 - - + -
808C LEU* 4.2 17.3 - - + +
811C PHE* 3.5 50.9 - - + -
817C ILE* 3.5 24.5 - - + +
820C ILE* 4.4 10.1 - - + -
821C LYS* 4.0 4.5 + - - -
828C LEU* 4.1 16.4 - - + -
832C MET* 4.3 15.9 - - - +
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Residues in contact with LEU 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 3.1 12.3 + - - +
717C LYS* 3.8 11.0 - - - +
719C MET* 1.3 78.4 - - - +
721C GLY* 1.3 59.7 + - - +
722C LYS* 4.1 16.4 - - + +
820C ILE* 4.2 17.5 - - + +
821C LYS* 3.7 33.6 + - - +
823C PHE 3.8 17.7 - - - +
824C ASP 3.8 3.4 - - - -
825C GLU* 3.4 46.4 - - - +
828C LEU* 3.4 27.1 - - + -
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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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717C LYS 3.2 2.2 + - - -
718C MET 3.2 8.9 + - - -
719C MET 2.9 8.6 + - - -
720C LEU* 1.3 80.2 - - - +
722C LYS* 1.3 64.0 + - - +
821C LYS* 4.4 7.4 - - - -
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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