Contacts of the helix formed by residues 712 - 720 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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666D SER* 4.1 9.6 - - - -
672D THR* 3.8 20.6 - - - +
673D LEU 2.9 17.8 + - - +
674D GLN* 3.8 33.7 - - + +
711D PHE* 1.3 78.8 - - - +
713D ARG* 1.3 67.2 + - - +
714D PRO* 3.8 15.0 - - + -
715D PHE* 3.2 21.5 + - + +
716D TYR* 3.9 3.5 - - - -
732D VAL* 3.8 14.6 - - + -
796D PHE* 4.0 30.5 - - + -
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Residues in contact with ARG 713 (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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711D PHE 3.8 0.6 + - - -
712D ILE* 1.3 69.8 - - - +
714D PRO* 1.3 76.4 - - + +
715D PHE 2.8 2.3 + - - -
716D TYR* 2.8 24.7 + - - +
717D LYS* 3.2 32.4 + - + +
728D ASP* 4.3 15.0 + - - +
731D SER* 3.5 25.1 + - - +
732D VAL* 4.4 2.2 - - - +
825D GLU* 3.1 42.7 + - - +
826D ASN* 5.1 15.0 + - - +
829D GLU* 5.5 7.2 - - - -
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Residues in contact with PRO 714 (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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712D ILE* 3.7 17.9 - - + -
713D ARG* 1.3 96.9 - - + +
715D PHE* 1.3 61.7 + - - +
717D LYS* 3.1 6.6 + - + +
718D MET* 3.0 32.8 + - + +
724D ILE* 3.7 38.0 - - + +
728D ASP* 4.1 14.4 - - + +
732D VAL* 3.9 10.1 - - + -
796D PHE* 4.2 22.0 - - + -
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Residues in contact with PHE 715 (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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663D PHE* 4.4 3.6 - + - -
673D LEU 5.2 0.4 - - - +
674D GLN* 5.4 0.9 - - - -
675D ILE* 3.9 28.5 - - + -
711D PHE* 3.8 55.0 - + + -
712D ILE* 3.2 22.2 + - + +
713D ARG 2.8 4.9 + - - -
714D PRO* 1.3 75.6 - - - +
716D TYR* 1.3 68.4 + + - +
718D MET* 3.1 20.8 + - + +
719D MET* 3.6 18.9 + - - +
804D MET* 3.5 33.3 - - + +
807D PHE* 4.0 31.9 - + - -
832D MET* 5.1 1.6 - - + -
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Residues in contact with TYR 716 (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 PHE* 4.0 0.9 - - - -
711D PHE* 3.1 52.0 + + + -
712D ILE 3.9 8.3 - - - -
713D ARG* 2.8 17.2 + - + +
715D PHE* 1.3 78.9 - + - +
717D LYS* 1.3 60.9 + - - +
719D MET* 3.7 2.7 + - - -
720D LEU* 3.3 28.4 + - - +
825D GLU* 4.1 22.2 - - + +
828D LEU* 3.9 26.4 - - + +
829D GLU* 3.4 45.2 - - + +
832D MET* 4.1 17.3 - - - -
833D CYS* 3.1 26.7 - - - -
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Residues in contact with LYS 717 (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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713D ARG* 3.2 39.6 + - + +
714D PRO* 3.1 9.3 + - + +
715D PHE 3.1 1.2 - - - -
716D TYR* 1.3 78.7 - - - +
718D MET* 1.3 62.1 + - - +
719D MET 3.2 0.9 - - - -
720D LEU* 3.9 5.6 - - - -
721D GLY 3.2 3.5 + - - -
722D LYS* 2.9 44.7 + - + +
723D GLN 3.1 20.3 + - - -
724D ILE* 3.9 8.7 - - + -
725D THR* 4.4 4.4 + - - +
728D ASP* 2.6 40.0 + - - +
825D GLU* 3.8 19.9 + - + +
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Residues in contact with MET 718 (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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675D ILE* 6.5 0.2 - - + -
714D PRO* 3.0 28.7 + - + +
715D PHE* 3.1 10.9 + - + +
717D LYS* 1.3 75.6 - - - +
719D MET* 1.3 64.2 + - - +
721D GLY* 3.7 8.2 + - - -
722D LYS 4.9 4.7 - - - +
724D ILE* 4.2 14.4 - - + -
796D PHE 3.0 30.3 - - - +
797D VAL* 4.3 10.1 - - + -
800D VAL* 4.1 8.7 - - + -
801D GLN* 3.7 26.9 - - - +
804D MET* 3.8 27.6 - - + -
808D LEU* 3.9 14.8 - - - +
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Residues in contact with MET 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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715D PHE* 3.6 20.6 + - + +
716D TYR* 3.9 6.7 - - - +
718D MET* 1.3 77.5 - - - +
720D LEU* 1.3 60.8 + - + +
721D GLY* 2.9 10.8 + - - -
804D MET* 3.9 17.5 - - + -
807D PHE* 3.7 15.0 - - + -
808D LEU* 4.0 14.8 - - + +
811D PHE* 3.4 51.8 - - + -
817D ILE* 4.1 24.3 - - + +
820D ILE* 5.3 2.2 - - + -
821D LYS* 4.4 1.7 - - - +
828D LEU* 3.7 25.8 - - + -
832D MET* 3.9 15.9 - - - +
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Residues in contact with LEU 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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716D TYR 3.3 15.1 + - - +
717D LYS* 4.1 4.0 - - - +
719D MET* 1.3 78.2 - - - +
721D GLY* 1.3 63.4 + - - +
722D LYS* 4.1 23.7 + - + +
820D ILE* 3.9 29.4 - - + +
821D LYS* 3.7 29.4 - - + +
823D PHE 3.9 14.4 - - - +
824D ASP* 3.3 10.3 - - - -
825D GLU* 3.0 50.0 - - + +
828D LEU* 4.2 13.0 - - + -
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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