Contacts of the helix formed by residues 753 - 765 (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 ALA 753 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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697B SER 3.9 21.1 - - - +
698B THR* 4.0 11.9 - - - +
749D PHE* 2.8 32.3 + - + +
750D MET 3.4 3.6 - - - +
752D GLU* 1.3 76.4 - - - +
754D ALA* 1.3 61.8 + - - +
755D ASP 2.9 5.4 + - - -
756D SER* 2.8 30.9 + - - +
757D TYR* 3.7 6.9 - - + -
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Residues in contact with ALA 754 (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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566D ILE* 5.4 1.4 - - - +
580D SER* 5.4 2.0 - - - +
581D SER* 3.5 35.4 + - - +
583D LEU* 4.3 8.1 - - + +
584D GLU* 4.4 9.4 - - + +
750D MET 2.9 13.2 + - - +
751D ALA 3.3 16.2 + - - +
752D GLU 3.5 1.4 + - - -
753D ALA* 1.3 76.5 - - - +
755D ASP* 1.3 60.2 + - - +
757D TYR* 3.5 21.1 + - - +
758D ARG* 3.8 7.8 + - - +
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Residues in contact with ASP 755 (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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698B THR 6.1 1.1 - - - +
580D SER* 4.2 19.1 + - - +
581D SER* 5.7 0.8 - - - -
753D ALA 2.9 1.8 + - - -
754D ALA* 1.3 78.8 - - - +
756D SER* 1.3 61.0 + - - +
758D ARG* 2.8 46.5 + - - +
759D MET* 2.9 40.4 + - + +
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Residues in contact with SER 756 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697B SER 5.5 0.2 + - - -
698B THR 6.2 0.9 - - - -
700B VAL* 3.5 38.3 - - - +
704B ASN* 4.9 2.1 - - - +
705D VAL 4.7 0.6 - - - +
753D ALA* 2.8 28.7 + - - +
755D ASP* 1.3 79.7 - - - +
757D TYR* 1.3 65.1 + - - +
759D MET* 3.2 9.4 - - - +
760D ASN* 3.0 28.8 + - - +
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Residues in contact with TYR 757 (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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566D ILE* 4.0 4.2 - - + +
583D LEU* 3.4 23.8 - - + -
705D VAL* 3.6 40.6 - - + -
706D SER 3.3 17.6 - - - +
708D PRO* 3.8 23.6 - - + +
746D THR* 5.6 2.9 - - - +
749D PHE* 4.5 13.1 - + - -
750D MET* 3.6 44.0 + - + +
753D ALA* 3.7 15.5 - - + -
754D ALA* 3.7 10.3 - - - +
755D ASP 3.2 0.8 - - - -
756D SER* 1.3 81.8 + - - +
758D ARG* 1.3 58.0 + - - +
760D ASN* 3.5 1.7 + - - +
761D ALA* 3.0 29.8 + - - +
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Residues in contact with ARG 758 (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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566D ILE* 2.9 40.0 - - + +
567D LEU* 3.8 5.6 - - + +
581D SER* 6.3 1.6 - - - -
754D ALA 3.8 3.0 + - - +
755D ASP* 2.8 51.8 + - - +
757D TYR* 1.3 76.7 - - - +
759D MET* 1.3 80.6 + - - +
761D ALA* 3.4 1.8 + - - +
762D GLU* 3.0 71.3 + - - +
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Residues in contact with MET 759 (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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700B VAL* 3.1 23.8 - - + +
701B PRO* 3.6 7.2 - - + +
702B PRO* 3.0 56.8 - - + +
704B ASN* 4.8 4.5 - - - +
755D ASP* 2.9 32.0 + - - +
756D SER* 3.2 13.7 - - - +
758D ARG* 1.3 92.0 - - - +
760D ASN* 1.3 62.8 + - - +
762D GLU* 3.4 6.8 + - - +
763D ARG* 3.0 23.4 + - - +
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Residues in contact with ASN 760 (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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704B ASN* 3.1 24.3 + - - +
703D ASN 3.2 19.2 + - - -
704D ASN* 3.6 6.0 - - - +
705D VAL 3.3 30.1 + - - +
706D SER* 3.1 20.2 + - - +
756D SER 3.0 11.0 + - - +
757D TYR 3.7 2.0 - - - +
759D MET* 1.3 80.7 - - - +
761D ALA* 1.3 63.6 + - - +
763D ARG* 3.0 27.7 + - - +
764D ILE* 3.0 31.8 + - - +
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Residues in contact with ALA 761 (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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557D LEU* 5.0 4.3 - - + -
561D CYS* 3.8 18.8 - - - -
566D ILE* 4.7 0.7 - - + -
567D LEU* 3.6 26.5 - - + -
706D SER* 3.8 14.8 + - - -
757D TYR 3.0 18.0 + - - +
758D ARG* 3.9 2.5 - - - +
760D ASN* 1.3 75.7 - - - +
762D GLU* 1.3 57.2 + - - +
764D ILE* 3.2 4.1 + - - -
765D LEU* 2.9 34.5 + - - +
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Residues in contact with GLU 762 (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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567D LEU* 3.4 24.4 - - + +
758D ARG* 3.0 55.4 + - - +
759D MET* 3.7 5.5 - - - +
761D ALA* 1.3 76.7 - - - +
763D ARG* 1.3 62.5 + - - +
765D LEU* 3.9 2.5 - - - -
766D ALA* 3.3 21.8 + - - +
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Residues in contact with ARG 763 (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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702B PRO 4.5 10.4 + - - +
703B ASN* 3.2 27.1 - - - +
704B ASN* 4.2 8.1 - - - +
763B ARG* 3.5 36.9 - - - +
703D ASN* 3.1 45.1 + - - +
759D MET 3.0 13.8 + - - +
760D ASN* 3.0 34.8 + - - +
762D GLU* 1.3 77.4 - - - +
764D ILE* 1.3 68.9 + - - +
766D ALA* 3.5 16.7 - - - +
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Residues in contact with ILE 764 (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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554D GLN* 4.7 8.1 + - - -
557D LEU* 3.9 20.9 - - + -
640D SER 3.6 16.2 - - - +
641D MET* 3.8 20.2 - - + +
703D ASN* 3.4 32.8 - - - +
706D SER* 3.5 12.8 - - - +
760D ASN* 3.0 39.0 + - - +
761D ALA 3.8 4.0 - - - +
763D ARG* 1.3 88.6 - - - +
765D LEU* 1.3 61.5 + - + +
766D ALA 3.3 2.3 + - - -
767D GLY 5.3 0.5 + - - -
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Residues in contact with LEU 765 (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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554D GLN* 4.0 26.9 - - + +
557D LEU* 3.8 35.2 - - + -
558D SER* 4.1 22.7 - - - +
567D LEU* 4.3 17.5 - - + -
761D ALA* 2.9 18.7 + - + +
762D GLU* 3.9 3.6 - - - +
764D ILE* 1.3 81.6 - - + +
766D ALA* 1.3 66.0 + - - +
767D GLY 3.4 2.0 - - - -
768D PHE* 3.1 40.9 + - + +
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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