Contacts of the helix formed by residues 753 - 766 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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697A SER 4.5 1.6 - - - +
698A THR* 4.2 20.2 - - - +
700A VAL* 6.4 0.2 - - + -
749C PHE* 2.9 40.0 + - + +
750C MET* 3.3 4.3 - - - +
752C GLU* 1.3 79.8 - - - +
754C ALA* 1.3 61.5 + - - +
755C ASP 3.0 4.0 + - - -
756C SER* 2.8 31.0 + - - +
757C TYR* 3.7 4.5 - - + -
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Residues in contact with ALA 754 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566C ILE* 5.7 0.5 - - - +
581C SER* 3.8 34.0 + - - +
583C LEU* 4.4 8.4 - - + +
584C GLU* 4.5 9.9 - - + +
750C MET 2.9 10.9 + - - +
751C ALA 3.4 15.9 + - - +
752C GLU 3.4 1.6 + - - -
753C ALA* 1.3 76.7 - - - +
755C ASP* 1.3 61.5 + - - +
756C SER 3.4 0.2 + - - -
757C TYR* 3.5 19.0 + - - +
758C ARG* 3.6 9.7 + - - +
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Residues in contact with ASP 755 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580C SER* 5.6 5.5 - - - -
581C SER* 6.1 0.4 - - - -
753C ALA 3.0 1.6 + - - -
754C ALA* 1.3 77.0 - - - +
756C SER* 1.3 60.9 + - - +
757C TYR 3.3 0.2 - - - -
758C ARG* 2.8 45.5 + - - +
759C MET* 2.9 42.3 + - + +
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Residues in contact with SER 756 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700A VAL* 3.3 31.0 - - - -
704A ASN* 5.2 6.8 + - - -
705C VAL 4.8 0.4 - - - +
749C PHE* 5.7 1.7 - - - -
753C ALA* 2.8 27.3 + - - +
755C ASP* 1.3 76.5 - - - +
757C TYR* 1.3 72.7 + - - +
759C MET* 3.4 13.9 + - - +
760C ASN* 3.1 23.0 + - - +
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Residues in contact with TYR 757 (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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566C ILE* 4.3 3.6 - - + -
583C LEU* 3.4 24.5 - - + -
696C GLU* 5.5 1.6 + - - -
705C VAL* 3.7 37.9 - - + -
706C SER 3.5 16.6 - - - +
708C PRO* 3.7 27.2 - - + +
746C THR* 5.4 5.2 - - - +
749C PHE* 4.0 20.2 - + - -
750C MET* 3.7 36.4 - - + +
753C ALA* 3.7 18.4 - - + -
754C ALA* 3.9 5.8 - - - +
755C ASP 3.3 0.2 - - - -
756C SER* 1.3 82.8 + - - +
758C ARG* 1.3 65.6 + - - +
760C ASN* 3.2 4.0 + - - +
761C ALA* 3.0 23.9 + - - +
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Residues in contact with ARG 758 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566C ILE* 3.0 38.7 - - + +
567C LEU* 4.0 6.0 - - + +
581C SER* 6.2 2.2 - - - -
754C ALA 3.6 6.7 + - - +
755C ASP* 2.8 49.4 + - - +
757C TYR* 1.3 79.6 - - - +
759C MET* 1.3 75.4 + - - +
761C ALA* 3.2 4.2 + - - +
762C GLU* 2.8 76.0 + - - +
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Residues in contact with MET 759 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700A VAL* 3.4 24.0 - - + +
701A PRO 4.1 5.6 - - - +
702A PRO* 3.6 42.4 - - + +
755C ASP* 2.9 34.7 + - + +
756C SER* 3.4 17.5 + - - +
758C ARG* 1.3 102.2 - - - +
760C ASN* 1.3 62.2 + - - +
762C GLU* 3.9 4.6 - - - +
763C ARG* 3.1 24.1 + - - +
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Residues in contact with ASN 760 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A PRO 5.6 0.7 - - - -
704A ASN* 3.5 15.3 + - - +
703C ASN 3.1 19.3 + - - -
704C ASN* 3.3 14.9 - - - +
705C VAL 3.3 27.9 + - - +
706C SER* 2.9 23.2 + - - +
756C SER 3.1 12.4 + - - +
757C TYR 3.2 5.1 + - - +
759C MET* 1.3 78.3 - - - +
761C ALA* 1.3 57.8 + - - +
763C ARG* 3.1 25.0 + - - +
764C ILE* 3.0 38.0 + - - +
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Residues in contact with ALA 761 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557C LEU* 4.8 3.6 - - + -
561C CYS* 3.7 29.6 - - - -
566C ILE* 4.7 2.2 - - + -
567C LEU* 3.8 12.3 - - + -
706C SER* 3.8 16.5 + - - -
757C TYR 3.0 15.4 + - - +
758C ARG 3.8 3.8 - - - +
760C ASN* 1.3 74.3 - - - +
762C GLU* 1.3 58.7 - - - +
764C ILE* 4.4 3.4 - - - +
765C LEU* 2.8 36.8 + - + +
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Residues in contact with GLU 762 (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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567C LEU* 3.3 26.4 - - + +
758C ARG* 2.8 55.2 + - - +
759C MET* 3.9 5.6 - - - +
761C ALA* 1.3 76.5 - - - +
763C ARG* 1.3 62.3 + - - +
765C LEU* 3.7 1.6 - - - -
766C ALA* 3.1 25.5 + - - +
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Residues in contact with ARG 763 (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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702A PRO 4.9 7.8 + - - +
703A ASN* 3.6 11.8 + - - -
704A ASN* 5.4 1.6 - - - +
763A ARG* 3.3 39.6 - - - +
703C ASN* 2.9 56.4 + - - +
704C ASN* 4.5 0.8 - - - +
759C MET 3.1 17.0 + - - +
760C ASN* 3.1 23.7 + - - +
761C ALA 3.2 0.2 - - - -
762C GLU* 1.3 79.1 - - - +
764C ILE* 1.3 68.2 + - - +
766C ALA* 3.5 15.5 + - - +
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Residues in contact with ILE 764 (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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554C GLN* 4.7 9.5 + - + +
557C LEU* 3.9 9.6 - - + -
640C SER 3.4 25.1 - - - +
641C MET* 3.5 29.2 - - + +
703C ASN* 3.5 24.0 - - - +
706C SER* 3.4 25.1 - - - +
760C ASN* 3.0 27.7 + - - +
761C ALA 4.0 2.9 - - - +
763C ARG* 1.3 88.9 - - - +
765C LEU* 1.3 62.2 + - + +
766C ALA 3.4 2.0 + - - +
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Residues in contact with LEU 765 (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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554C GLN* 4.1 25.8 - - + +
557C LEU* 3.9 28.0 - - + +
558C SER* 3.8 30.5 - - - +
567C LEU* 3.9 24.7 - - + -
761C ALA* 2.8 16.3 + - + +
762C GLU* 3.7 2.9 - - - +
764C ILE* 1.3 81.7 - - + +
766C ALA* 1.3 65.2 + - - +
767C GLY 3.2 0.7 + - - -
768C PHE* 2.9 40.9 + - + +
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Residues in contact with ALA 766 (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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762C GLU 3.1 15.9 + - - +
763C ARG* 3.5 11.4 + - - +
764C ILE 3.4 4.8 - - - +
765C LEU* 1.3 76.6 - - - +
767C GLY* 1.3 63.6 + - - +
768C PHE* 3.2 1.0 + - - +
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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