Contacts of the helix formed by residues 752 - 763 (chain D) in PDB entry 6OY5
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 SER 752 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1047C HIS* 5.0 1.9 - - - +
1051C GLU* 2.6 25.0 + - - +
1075C ASP* 4.1 10.3 - - - -
1076C VAL* 3.7 20.0 - - - -
751D LEU* 1.3 78.0 - - - +
753D SER* 1.3 59.0 - - - +
754D PHE* 3.2 11.2 + - - +
755D ALA* 2.8 20.8 + - - +
756D GLN* 2.9 29.6 + - - +
28E GLN* 5.4 2.9 - - - -
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Residues in contact with SER 753 (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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1075C ASP* 3.7 25.0 + - - -
752D SER* 1.3 74.0 - - - +
754D PHE* 1.3 57.1 + - - +
756D GLN* 3.9 6.0 - - - +
757D ALA* 3.0 29.3 + - - +
24E ALA* 4.3 4.0 - - - +
27E ALA* 4.6 10.3 - - - +
28E GLN* 4.1 15.9 - - - -
31E LEU* 3.7 20.6 - - - +
60E ALA* 5.3 0.9 - - - +
61E VAL* 4.0 16.1 - - - +
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Residues in contact with PHE 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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1047C HIS* 3.4 57.4 - + + -
752D SER* 3.1 10.5 + - - +
753D SER* 1.3 80.1 - - - +
755D ALA* 1.3 61.6 + - - +
757D ALA* 3.4 1.7 + - - +
758D GLU* 3.0 32.3 + - + +
1476D THR* 4.3 13.5 - - + -
20E THR* 4.7 1.1 - - + -
21E VAL* 4.3 28.7 - - + -
24E ALA* 3.7 26.2 - - + -
25E LYS* 4.5 17.3 - - + -
28E GLN* 3.9 23.1 - - - +
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Residues in contact with ALA 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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1047C HIS* 4.5 1.2 - - - +
1048C THR* 3.3 32.3 + - - +
1051C GLU* 3.6 19.5 - - - +
750D PRO* 3.5 20.4 - - + +
752D SER* 2.8 20.3 + - - +
754D PHE* 1.3 73.9 - - - +
756D GLN* 1.3 66.5 + - - +
758D GLU* 3.2 2.9 + - - -
759D ALA* 2.9 22.5 + - - +
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Residues in contact with GLN 756 (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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698D LYS* 3.3 28.0 - - + +
699D VAL* 2.4 45.7 + - - +
749D VAL* 5.7 0.4 - - - +
750D PRO* 2.8 36.5 + - - +
751D LEU 4.8 2.2 + - - -
752D SER 2.9 15.5 + - - +
753D SER* 3.9 6.5 - - - +
755D ALA* 1.3 76.5 - - - +
757D ALA* 1.3 62.7 + - - +
759D ALA* 3.1 3.7 + - - +
760D ARG* 2.9 45.3 + - - +
59E ASN* 5.4 1.1 - - - +
61E VAL* 4.5 10.3 - - + -
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Residues in contact with ALA 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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753D SER 3.0 19.5 + - - +
754D PHE 3.7 4.3 - - - +
756D GLN* 1.3 76.8 - - - +
758D GLU* 1.3 62.4 + - - +
760D ARG* 4.9 1.1 - - - -
761D ILE* 3.1 31.5 + - + +
20E THR* 3.6 18.0 - - + +
23E VAL* 4.5 5.8 - - + -
24E ALA* 3.9 20.0 - - + +
61E VAL* 4.3 19.2 - - + +
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Residues in contact with GLU 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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1045C ALA* 3.1 24.1 - - + +
1046C ALA 2.8 8.4 + - - -
1047C HIS* 2.8 18.8 + - - +
1048C THR* 2.7 39.5 + - - +
754D PHE* 3.0 15.7 + - + +
755D ALA 3.6 5.2 - - - +
757D ALA* 1.3 74.9 - - - +
759D ALA* 1.3 57.6 + - - +
762D GLN* 2.8 51.8 + - - +
763D MET* 3.3 3.3 + - - +
1476D THR* 2.4 33.1 + - + -
20E THR* 3.5 8.5 - - + +
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Residues in contact with ALA 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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1048C THR* 5.3 0.9 - - - +
699D VAL* 3.6 19.1 - - + -
701D LEU* 4.0 23.8 - - + -
715D ALA* 3.6 5.7 - - + +
750D PRO* 4.3 7.2 - - + -
755D ALA 2.9 17.4 + - - +
756D GLN 3.6 3.6 - - - +
758D GLU* 1.3 76.9 - - - +
760D ARG* 1.3 62.9 + - - +
763D MET* 3.0 19.2 + - - -
764D LEU 3.0 23.7 + - - -
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Residues in contact with ARG 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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697D GLY* 3.1 27.9 + - - -
699D VAL* 3.5 25.8 - - + -
717D GLN* 4.7 4.8 - - - +
756D GLN* 2.9 31.3 + - - +
757D ALA* 4.3 2.9 - - - +
759D ALA* 1.3 70.8 - - - +
761D ILE* 1.3 61.2 + - + +
764D LEU* 3.2 30.0 - - + +
767D HIS* 3.2 11.7 - - - -
3E GLU* 2.9 43.4 + - + +
59E ASN* 3.1 29.1 + - - +
61E VAL* 3.3 27.6 - - + +
62E THR* 3.2 26.1 + - - +
65E MET* 5.0 2.2 - - - -
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Residues in contact with ILE 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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757D ALA* 3.1 17.4 + - - +
760D ARG* 1.3 81.4 - - + +
762D GLN* 1.3 69.5 + - + +
767D HIS* 2.9 28.7 + - - +
6E ILE* 4.3 2.2 - - + -
10E PHE* 3.7 33.2 - - + -
16E LYS* 5.2 3.6 - - + +
19E LEU* 4.0 18.6 - - + -
20E THR* 3.9 35.2 - - + +
23E VAL* 4.3 17.5 - - + -
65E MET* 4.0 25.1 - - + -
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Residues in contact with GLN 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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1043C TYR* 2.9 36.0 + - + +
1044C GLY 3.4 12.1 + - - -
1045C ALA* 4.0 4.0 - - - +
758D GLU* 2.8 23.6 + - - +
761D ILE* 1.3 78.4 - - + +
763D MET* 1.3 63.3 + - + +
764D LEU 3.5 0.4 - - - -
767D HIS* 5.3 0.2 - - - +
768D ASN* 3.2 21.7 + - - +
1476D THR* 3.3 20.3 - - - +
10E PHE* 6.1 0.4 - - - -
16E LYS* 5.0 18.5 + - + +
17E TYR* 3.1 25.3 - - + -
20E THR* 2.8 31.7 + - - +
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Residues in contact with MET 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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1040C LEU* 3.7 14.1 - - + -
1043C TYR* 3.2 45.0 + - + -
1045C ALA* 4.0 21.5 - - + -
1048C THR* 5.1 3.1 - - - -
701D LEU* 3.7 19.7 - - + -
713D ILE* 3.5 33.2 - - + +
714D GLN* 3.4 8.2 - - - +
715D ALA* 2.8 28.9 + - + -
758D GLU 4.0 6.3 - - - +
759D ALA* 3.0 23.8 + - - +
762D GLN* 1.3 79.4 - - + +
764D LEU* 1.3 60.4 + - - +
768D ASN* 3.9 2.7 - - - -
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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