Contacts of the helix formed by residues 710 - 718 (chain D) in PDB entry 3T6A
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 LEU 710 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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564D ALA* 4.8 5.2 - - + -
583D LEU* 3.9 20.2 - - + -
586D ILE* 3.4 32.1 - - + -
598D ILE* 3.9 30.1 - - + -
645D TYR* 4.2 16.2 - - + -
696D GLU* 4.5 2.8 + - - -
707D VAL* 4.3 15.3 - - + -
708D PRO* 3.4 25.4 - - + +
709D LEU* 1.3 77.7 - - - +
711D MET* 1.3 58.6 + - - +
712D PRO* 3.5 2.5 - - - -
713D LEU* 3.2 13.1 + - + +
714D VAL* 2.9 32.4 + - + +
750D MET* 4.1 6.5 - - + -
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Residues in contact with MET 711 (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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598D ILE* 4.2 12.1 - - - +
599D ILE* 3.8 37.5 - - + +
602D HIS* 3.7 57.4 - - + +
603D ASN* 4.7 1.1 - - - +
645D TYR* 4.3 4.5 - - - -
648D SER* 4.7 4.5 - - - +
709D LEU* 2.7 14.6 + - + +
710D LEU* 1.3 72.7 - - - +
712D PRO* 1.3 70.8 - - + +
714D VAL* 3.4 1.6 + - - +
715D THR* 3.1 35.9 + - + +
723D THR* 4.2 17.3 - - + -
728D ASP* 4.1 15.9 - - - +
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Residues in contact with PRO 712 (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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692D HIS* 4.2 16.4 - - + +
709D LEU* 3.5 33.0 - - + -
710D LEU 3.9 1.3 - - - +
711D MET* 1.3 95.8 - - + +
713D LEU* 1.3 61.8 + - - +
715D THR* 3.2 7.8 + - - +
716D LEU* 3.0 24.8 + - - +
728D ASP* 3.9 14.6 - - - +
730D TRP* 3.3 18.7 + - + +
743D HIS* 3.5 25.1 - - + +
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Residues in contact with LEU 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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737C CYS* 3.8 12.6 - - - -
586D ILE* 4.4 11.0 - - + -
587D THR* 4.8 0.7 - - + -
710D LEU* 3.2 15.3 + - + +
712D PRO* 1.3 77.9 - - - +
714D VAL* 1.3 61.2 + - + +
716D LEU* 3.2 7.9 + - + +
717D MET* 3.0 41.1 + - + +
743D HIS* 4.5 20.6 + - + +
744D LEU* 3.7 25.6 - - + -
747D ALA* 3.4 35.2 - - + -
750D MET* 3.8 22.7 - - + -
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Residues in contact with VAL 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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586D ILE* 4.6 16.8 - - + -
595D ARG* 3.6 40.2 - - + +
598D ILE* 4.4 16.8 - - + -
599D ILE* 3.0 39.9 - - + -
710D LEU* 2.9 20.3 + - + +
711D MET* 3.9 5.2 - - - +
713D LEU* 1.3 80.7 - - + +
715D THR* 1.3 55.7 + - - +
717D MET* 3.4 1.7 + - - -
718D GLU* 3.1 29.3 + - - +
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Residues in contact with THR 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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719C ARG* 3.1 24.8 + - - -
599D ILE* 4.3 11.2 - - + -
711D MET* 3.1 34.4 + - + +
712D PRO* 3.2 1.0 + - - +
714D VAL* 1.3 75.1 - - - +
716D LEU* 1.3 66.3 + - - +
718D GLU* 3.4 11.4 + - - +
721D ALA* 4.5 1.8 - - + -
723D THR* 4.4 10.5 - - + -
728D ASP* 3.2 33.5 + - + +
729D MET* 4.3 8.1 - - + -
730D TRP* 3.2 17.1 + - - -
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Residues in contact with LEU 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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716C LEU* 4.3 30.5 - - + +
719C ARG* 4.7 6.3 + - - +
740C MET* 5.0 3.1 - - - -
712D PRO 3.0 15.2 + - - +
713D LEU* 3.3 11.9 - - + +
715D THR* 1.3 80.9 + - - +
717D MET* 1.3 60.2 + - + +
718D GLU 3.5 0.2 + - - -
719D ARG* 4.4 10.0 - - - +
730D TRP* 3.8 33.0 - - + +
740D MET* 3.8 46.0 - - + +
743D HIS* 5.4 4.0 - - + -
744D LEU* 4.2 27.4 - - + -
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Residues in contact with MET 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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730C TRP* 4.3 4.9 - - - +
735C GLN* 3.1 52.0 + - + +
736C SER* 4.3 0.2 - - - -
737C CYS* 3.5 26.5 - - - +
740C MET* 3.4 38.8 - - + -
586D ILE 3.6 14.6 - - - +
587D THR 4.4 1.6 - - - +
595D ARG* 3.5 31.6 - - - +
713D LEU* 3.0 28.3 + - + +
714D VAL* 3.9 4.9 - - - +
716D LEU* 1.3 77.8 - - + +
718D GLU* 1.3 59.9 + - - +
719D ARG* 3.8 4.9 + - - +
744D LEU* 5.2 0.2 - - + -
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Residues in contact with GLU 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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719C ARG* 2.8 15.9 + - - -
735C GLN* 3.1 13.6 + - - +
592D HIS* 2.6 45.5 + - - -
595D ARG* 2.7 41.1 + - + +
596D LEU* 3.9 10.7 - - + +
599D ILE* 4.3 6.3 - - + -
714D VAL 3.1 18.1 + - - +
715D THR 3.4 4.3 + - - +
716D LEU 3.3 0.8 - - - -
717D MET* 1.3 76.3 - - - +
719D ARG* 1.3 59.5 + - - +
720D GLN* 3.1 5.6 + - - +
721D ALA* 2.9 28.4 + - + +
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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