Contacts of the helix formed by residues 752 - 762 (chain N) in PDB entry 5X22
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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1047M HIS* 4.8 2.8 - - - +
1051M GLU* 2.7 25.6 + - - +
1075M ASP* 5.0 5.2 - - - -
1076M VAL* 3.5 24.8 - - - +
751N LEU* 1.3 77.5 - - - +
753N SER* 1.3 59.2 + - - +
754N PHE* 3.4 11.3 + - - +
755N ALA* 2.8 27.0 + - - +
756N GLN* 2.9 28.5 + - - +
28O GLN* 5.7 2.5 - - - -
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Residues in contact with SER 753 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1075M ASP* 3.7 10.0 + - - -
751N LEU 3.8 0.4 + - - -
752N SER* 1.3 73.0 - - - +
754N PHE* 1.3 56.8 + - - +
756N GLN* 3.7 7.7 - - - +
757N ALA* 2.9 28.8 + - - +
24O ALA* 4.2 4.2 - - - +
27O ALA* 4.4 9.7 - - - +
28O GLN* 4.4 20.4 - - - -
31O LEU* 3.5 26.5 - - - +
60O ALA* 5.2 1.2 - - - +
61O VAL* 3.8 18.5 - - - +
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Residues in contact with PHE 754 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1047M HIS* 3.3 55.0 - + + -
752N SER* 3.0 10.6 - - - +
753N SER* 1.3 76.5 - - - +
755N ALA* 1.3 61.0 + - - +
757N ALA* 3.1 4.9 + - - +
758N GLU* 2.9 36.6 + - + +
1476N THR* 4.6 3.8 - - + -
1482N ARG 6.0 0.2 - - - -
20O THR* 5.1 0.7 - - + -
21O VAL* 4.0 40.2 - - + -
24O ALA* 3.5 27.1 - - + -
25O LYS* 4.4 15.9 - - + -
28O GLN* 3.7 24.5 - - - +
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Residues in contact with ALA 755 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1047M HIS* 4.3 1.4 - - - +
1048M THR* 3.4 31.3 + - - +
1051M GLU* 3.4 25.1 - - - +
750N PRO* 3.7 12.7 - - + +
752N SER* 2.8 23.1 + - - +
754N PHE* 1.3 72.8 - - - +
756N GLN* 1.3 58.1 + - - +
758N GLU* 3.3 5.8 + - - -
759N ALA* 2.9 29.8 + - - +
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Residues in contact with GLN 756 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653N PHE* 6.4 0.2 - - - -
698N LYS* 3.2 29.0 - - + +
699N VAL* 2.5 45.1 + - - +
749N VAL* 5.4 0.6 - - - +
750N PRO* 2.9 41.0 + - - +
751N LEU 4.7 2.2 + - - +
752N SER 2.9 15.9 + - - +
753N SER* 3.7 9.2 - - - +
755N ALA* 1.3 77.9 - - - +
757N ALA* 1.3 55.9 + - - +
759N ALA* 3.8 1.4 - - - +
760N ARG* 2.9 48.7 + - - +
59O ASN* 5.2 2.9 - - - +
61O VAL* 4.6 9.0 - - + -
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Residues in contact with ALA 757 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753N SER 2.9 16.0 + - - +
754N PHE 3.1 9.8 + - - +
756N GLN* 1.3 73.7 - - - +
758N GLU* 1.3 64.0 - - - +
760N ARG* 3.3 1.0 + - - -
761N ILE* 2.9 31.7 + - + +
20O THR* 3.8 18.4 - - + +
23O VAL* 4.4 10.8 - - + -
24O ALA* 3.9 20.0 - - + +
61O VAL* 4.4 11.6 - - + +
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Residues in contact with GLU 758 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045M ALA* 3.2 18.4 - - + +
1046M ALA 3.6 4.5 - - - -
1047M HIS* 2.9 30.3 + - - -
1048M THR* 2.9 31.0 + - - +
754N PHE* 2.9 14.9 + - + +
755N ALA* 3.3 6.2 + - - +
757N ALA* 1.3 74.9 - - - +
759N ALA* 1.3 57.9 + - - +
762N GLN* 2.9 34.6 + - - +
763N MET* 3.3 8.1 + - - +
1476N THR* 2.3 34.8 + - + -
20O THR* 3.6 20.6 - - + -
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Residues in contact with ALA 759 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1048M THR* 4.9 2.0 + - + +
699N VAL* 3.6 21.3 - - + -
701N LEU* 4.2 21.8 - - + -
715N ALA* 3.5 4.7 - - - +
750N PRO* 4.3 8.5 - - + -
755N ALA 2.9 17.4 + - - +
756N GLN 3.8 1.1 - - - +
758N GLU* 1.3 76.8 - - - +
760N ARG* 1.3 60.0 + - - +
763N MET* 3.2 17.8 + - - -
764N LEU 2.9 27.5 + - - -
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Residues in contact with ARG 760 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697N GLY* 3.5 21.6 + - - -
699N VAL* 3.6 27.6 - - + +
717N GLN* 5.1 3.2 - - - +
756N GLN* 2.9 33.8 + - - +
757N ALA* 4.0 3.6 - - - +
759N ALA* 1.3 75.9 - - - +
761N ILE* 1.3 61.3 + - + +
764N LEU* 3.4 12.0 - - - +
767N HIS* 3.2 20.3 - - - -
3O GLU* 3.1 42.9 + - - +
59O ASN* 3.1 22.8 + - - +
61O VAL* 3.5 15.0 - - + +
62O THR* 3.0 46.5 + - - +
65O MET* 4.4 4.0 - - - -
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Residues in contact with ILE 761 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757N ALA* 2.9 20.4 + - - +
760N ARG* 1.3 81.2 - - + +
762N GLN* 1.3 66.9 + - + +
763N MET 3.6 0.2 - - - -
764N LEU 4.3 0.2 + - - -
767N HIS* 2.5 31.3 + - - +
6O ILE* 4.4 2.7 - - + -
10O PHE* 3.7 33.5 - - + -
16O LYS* 4.8 1.6 - - + +
19O LEU* 4.1 12.3 - - + -
20O THR* 3.7 38.6 - - + +
23O VAL* 3.9 26.9 - - + -
65O MET* 4.3 21.3 - - + -
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Residues in contact with GLN 762 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1043M TYR* 2.8 35.5 + - + +
1044M GLY 3.2 16.0 + - - -
1045M ALA* 3.7 7.5 - - - +
758N GLU* 2.9 16.5 + - - +
761N ILE* 1.3 78.2 - - + +
763N MET* 1.3 64.0 + - + +
767N HIS* 4.8 1.7 - - - +
768N ASN* 3.4 23.9 + - - +
1476N THR* 3.2 22.3 - - - +
16O LYS* 4.6 22.2 + - - +
17O TYR* 3.3 16.5 - - + -
20O THR* 2.9 28.9 + - - +
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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