Contacts of the helix formed by residues 753 - 765 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749B PHE* 3.0 36.5 + - + +
750B MET 3.5 3.8 - - - +
751B ALA 3.3 0.2 - - - -
752B GLU* 1.3 76.8 - - - +
754B ALA* 1.3 61.0 + - - -
755B ASP* 3.2 4.0 + - - +
756B SER* 2.9 31.2 + - - +
757B TYR* 3.3 8.8 - - + -
697D SER 4.7 8.3 - - - +
698D THR* 4.9 11.7 - - - +
700D VAL* 5.6 3.1 - - + -
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Residues in contact with ALA 754 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B ILE* 5.6 0.9 - - - +
581B SER* 3.5 36.5 + - - +
583B LEU* 4.4 8.2 - - + +
584B GLU* 4.6 7.2 - - + +
750B MET 3.2 11.3 + - - +
751B ALA 3.8 13.7 - - - +
752B GLU 3.3 4.8 + - - -
753B ALA* 1.3 76.9 - - - +
755B ASP* 1.3 61.6 + - - +
757B TYR* 3.3 20.3 + - - +
758B ARG* 3.5 10.1 + - - +
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Residues in contact with ASP 755 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752B GLU 5.1 0.6 + - - -
753B ALA 3.2 1.2 - - - -
754B ALA* 1.3 77.3 - - - +
756B SER* 1.3 66.2 + - - +
758B ARG* 3.0 43.7 + - - +
759B MET* 2.9 35.6 + - + +
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Residues in contact with SER 756 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705B VAL 5.3 0.4 - - - -
753B ALA* 2.9 28.8 + - - +
755B ASP* 1.3 77.4 - - - +
757B TYR* 1.3 70.9 + - - +
759B MET* 3.5 13.2 + - - +
760B ASN* 3.0 24.8 + - - +
700D VAL* 3.7 28.7 - - - -
704D ASN* 4.6 10.6 + - - -
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Residues in contact with TYR 757 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566B ILE* 4.4 2.9 - - + -
583B LEU* 3.5 21.8 - - + -
696B GLU* 5.6 0.2 + - - -
705B VAL* 3.5 42.8 - - + -
706B SER 3.7 15.5 - - - +
708B PRO* 4.0 22.6 - - + +
746B THR* 5.5 3.5 - - - +
749B PHE* 4.4 14.0 - + - -
750B MET* 3.8 40.3 - - + +
753B ALA* 3.3 29.6 - - + -
754B ALA* 3.3 8.0 + - - +
755B ASP 3.2 0.4 - - - -
756B SER* 1.3 87.9 + - - +
758B ARG* 1.3 62.9 + - - +
760B ASN* 3.3 2.8 + - - +
761B ALA* 3.0 24.4 + - - +
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Residues in contact with ARG 758 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B ILE* 3.1 37.4 - - + +
567B LEU* 3.7 5.9 - - + +
754B ALA 3.5 5.3 + - - +
755B ASP* 3.0 49.4 + - - +
757B TYR* 1.3 79.3 - - - +
759B MET* 1.3 78.6 + - - +
761B ALA* 3.3 4.5 + - - +
762B GLU* 2.8 67.9 + - - +
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Residues in contact with MET 759 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755B ASP* 2.9 22.8 + - + +
756B SER* 3.9 23.6 - - - +
758B ARG* 1.3 96.8 - - - +
760B ASN* 1.3 62.3 + - - +
762B GLU* 3.2 11.9 + - - +
763B ARG* 3.0 25.8 + - - +
700D VAL* 4.0 13.7 - - + +
701D PRO 3.6 22.9 - - - +
702D PRO* 3.6 35.0 - - + +
704D ASN 5.6 0.2 - - - +
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Residues in contact with ASN 760 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703B ASN 3.4 14.9 + - - -
704B ASN* 3.2 22.6 + - - +
705B VAL 3.5 21.8 - - - +
706B SER* 2.7 25.2 + - - +
756B SER 3.0 19.0 + - - +
757B TYR 3.6 4.9 - - - +
758B ARG 3.3 0.2 - - - -
759B MET* 1.3 76.7 - - - +
761B ALA* 1.3 61.7 + - - +
763B ARG* 3.0 28.4 + - - +
764B ILE* 3.2 33.6 + - - +
704D ASN* 5.6 2.0 + - - +
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Residues in contact with ALA 761 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557B LEU* 4.9 4.3 - - + -
561B CYS* 3.7 29.8 - - - -
566B ILE* 4.8 0.9 - - + -
567B LEU* 4.1 11.0 - - + -
706B SER* 3.7 18.1 + - - +
757B TYR 3.0 15.8 + - - +
758B ARG* 3.3 4.9 + - - +
760B ASN* 1.3 74.9 - - - +
762B GLU* 1.3 64.2 - - - +
764B ILE* 3.4 3.3 + - - +
765B LEU* 3.0 30.2 + - + +
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Residues in contact with GLU 762 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567B LEU* 3.7 18.6 - - + +
758B ARG* 2.8 54.0 + - - +
759B MET* 3.2 11.2 + - - +
761B ALA* 1.3 75.8 - - - +
763B ARG* 1.3 63.5 + - - +
765B LEU* 3.4 3.7 + - - -
766B ALA* 3.2 25.1 + - - +
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Residues in contact with ARG 763 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703B ASN* 3.2 42.4 + - - +
704B ASN* 4.8 0.2 - - - +
759B MET 3.0 15.9 + - - +
760B ASN* 3.0 32.2 + - - +
762B GLU* 1.3 80.2 - - - +
764B ILE* 1.3 69.0 + - - +
765B LEU 3.3 0.3 + - - -
766B ALA* 3.6 14.6 + - - +
703D ASN* 4.1 9.6 + - - -
763D ARG* 3.5 40.6 - - - +
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Residues in contact with ILE 764 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554B GLN* 5.1 7.3 + - - -
557B LEU* 3.8 20.9 - - + -
640B SER 3.4 24.0 - - - +
641B MET* 3.5 21.3 - - + +
703B ASN* 3.4 24.7 - - - +
706B SER* 3.4 24.2 - - - +
760B ASN* 3.2 23.6 + - - +
761B ALA 3.9 4.0 - - - +
762B GLU 3.3 0.2 - - - -
763B ARG* 1.3 91.0 - - - +
765B LEU* 1.3 61.5 + - + +
766B ALA 3.7 0.3 + - - -
767B GLY 5.2 0.7 + - - -
768B PHE* 5.3 1.0 - - - +
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Residues in contact with LEU 765 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554B GLN* 4.0 24.0 - - + +
557B LEU* 3.9 24.0 - - + +
558B SER* 4.0 24.9 - - - -
567B LEU* 4.2 19.3 - - + -
761B ALA* 3.0 19.7 + - + +
762B GLU* 3.8 3.8 - - - +
763B ARG 3.2 0.4 - - - -
764B ILE* 1.3 80.0 - - + +
766B ALA* 1.3 64.7 + - - +
767B GLY 3.4 2.7 - - - -
768B PHE* 3.0 49.9 + - + +
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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