Contacts of the helix formed by residues 696 - 713 (chain A) in PDB entry 5YPO
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 696 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660A GLU 3.8 10.1 - - - -
661A ILE* 4.2 7.1 - - - +
663A LYS* 6.1 2.2 - - - -
694A GLY 3.7 0.6 - - - -
695A ASP* 1.3 78.4 - - - +
697A PHE* 1.3 65.3 + - - +
698A GLU* 3.6 16.4 + - - +
699A GLU* 3.1 24.5 + - - +
700A ILE* 3.1 25.3 + - - +
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Residues in contact with PHE 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543A THR* 3.6 34.3 - - + -
546A ARG* 3.5 54.7 - - + +
547A ALA* 3.8 24.2 - - + -
550A ASP* 3.5 21.3 - - - -
660A GLU 4.5 0.6 + - - -
661A ILE* 3.5 20.3 + - - +
696A SER* 1.3 74.4 - - - +
698A GLU* 1.3 64.3 + - - +
700A ILE* 3.1 8.9 + - + +
701A TYR* 2.7 62.9 + + + +
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Residues in contact with GLU 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546A ARG* 4.2 17.7 + - - -
696A SER* 3.6 19.6 - - - +
697A PHE* 1.3 87.7 + - + +
699A GLU* 1.3 59.9 + - - +
701A TYR* 4.1 3.4 - - - +
702A HIS* 3.1 26.7 + - - +
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Residues in contact with GLU 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A GLY* 3.5 14.4 - - - -
695A ASP* 2.9 28.9 + - - +
696A SER* 3.1 21.6 + - - +
698A GLU* 1.3 78.3 - - - +
700A ILE* 1.3 63.4 + - - +
702A HIS* 3.5 4.4 + - - +
703A LYS* 3.0 56.6 + - + +
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Residues in contact with ILE 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543A THR* 4.4 5.8 - - - +
547A ALA* 5.9 0.4 - - + -
650A ILE* 3.6 47.3 - - + -
661A ILE* 4.0 20.9 - - + -
692A VAL* 3.6 14.9 - - + +
693A GLU* 3.5 10.3 - - - -
694A GLY* 3.4 30.5 - - - +
696A SER 3.1 16.1 + - - +
697A PHE* 3.5 13.0 - - + +
699A GLU* 1.3 75.1 - - - +
701A TYR* 1.3 59.0 + - - +
703A LYS* 3.1 4.9 + - - +
704A VAL* 2.8 27.8 + - + +
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Residues in contact with TYR 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A ALA* 3.9 16.8 - - + -
550A ASP* 3.2 43.7 + - + +
551A LEU* 3.3 23.5 + - + -
554A GLU* 2.6 31.4 + - - +
697A PHE* 2.7 51.3 + + + +
698A GLU* 4.1 4.0 - - - +
700A ILE* 1.3 75.5 - - - +
702A HIS* 1.3 64.4 + - - +
704A VAL* 3.1 6.8 + - + +
705A LYS* 3.0 48.8 + - + +
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Residues in contact with HIS 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698A GLU 3.1 18.2 + - - +
699A GLU* 3.8 4.8 + - - +
701A TYR* 1.3 78.7 - - - +
703A LYS* 1.3 67.8 + - - +
705A LYS* 3.3 20.6 + - + +
706A ARG* 3.1 36.2 + - + +
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Residues in contact with LYS 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692A VAL* 3.9 20.9 - - + -
693A GLU* 2.6 35.8 + - - +
699A GLU* 3.0 42.2 + - + +
700A ILE 3.1 7.6 + - - +
702A HIS* 1.3 78.5 - - - +
704A VAL* 1.3 65.9 + - - +
706A ARG* 3.2 7.0 + - - +
707A VAL* 3.0 27.4 + - + +
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Residues in contact with VAL 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A ILE* 3.8 27.8 - - + -
547A ALA* 5.0 5.4 - - + -
551A LEU* 4.3 8.5 - - + -
648A ILE* 4.1 24.5 - - + -
650A ILE* 4.3 21.8 - - + -
692A VAL* 4.4 7.0 - - + -
700A ILE* 2.8 22.3 + - + +
701A TYR* 3.1 12.5 + - + +
703A LYS* 1.3 72.2 - - - +
705A LYS* 1.3 63.1 + - + +
707A VAL* 3.2 5.4 + - - +
708A ILE* 3.1 36.2 + - + +
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Residues in contact with LYS 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A LEU* 3.7 19.7 - - + -
554A GLU* 2.9 26.7 + - - -
555A PHE* 3.8 23.6 - - + -
701A TYR* 3.0 47.6 + - + +
702A HIS* 3.7 20.2 - - + +
703A LYS 3.2 0.2 - - - -
704A VAL* 1.3 76.4 - - - +
706A ARG* 1.3 57.6 + - + +
708A ILE* 3.6 6.7 + - - +
709A GLU* 3.1 43.7 + - - +
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Residues in contact with ARG 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702A HIS* 3.1 32.4 + - + +
703A LYS* 3.2 9.4 + - - +
705A LYS* 1.3 77.4 - - + +
707A VAL* 1.3 59.5 + - - +
709A GLU* 3.0 53.4 + - - +
710A ASP* 2.7 76.2 + - - +
573B TYR* 4.2 5.2 - - - +
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Residues in contact with VAL 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646A ILE* 4.3 1.8 - - + -
648A ILE* 3.7 23.3 - - + -
689A SER* 5.6 0.2 - - - -
690A ALA* 3.8 25.8 - - + -
692A VAL* 4.0 16.2 - - + -
703A LYS* 3.0 19.5 + - + +
704A VAL 3.6 6.7 - - - +
706A ARG* 1.3 75.0 - - - +
708A ILE* 1.3 64.2 + - - +
710A ASP* 3.9 0.3 - - - +
711A LEU* 2.9 42.8 + - + +
573B TYR* 3.7 33.0 - - + -
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Residues in contact with ILE 708 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537A ILE* 4.0 26.9 - - + -
551A LEU* 3.7 34.1 - - + -
559A PHE* 3.8 32.3 - - + -
625A HIS* 4.2 5.6 - - + +
646A ILE* 4.4 7.2 - - + -
648A ILE* 4.0 12.8 - - + -
704A VAL* 3.1 23.1 + - + +
705A LYS* 3.9 4.5 - - - +
706A ARG 3.3 0.2 - - - -
707A VAL* 1.3 76.4 - - - +
709A GLU* 1.3 60.7 + - + +
711A LEU* 3.7 0.7 - - - +
712A SER* 2.8 45.1 + - - +
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Residues in contact with GLU 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A PHE* 5.4 6.9 - - - -
705A LYS* 3.1 29.4 + - - +
706A ARG* 3.0 36.8 + - - +
708A ILE* 1.3 79.5 - - + +
710A ASP* 1.3 59.7 + - - +
712A SER* 4.6 3.4 - - - -
713A GLY* 3.1 22.7 + - - -
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Residues in contact with ASP 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706A ARG* 2.7 57.0 + - - +
709A GLU* 1.3 78.6 - - - +
711A LEU* 1.3 62.4 + - + +
712A SER 3.5 0.2 + - - -
713A GLY* 4.1 8.7 + - - -
573B TYR* 2.8 37.8 + - + -
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Residues in contact with LEU 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535A ARG* 3.7 21.4 + - - +
646A ILE* 4.1 20.6 - - + -
689A SER* 3.9 21.5 - - - -
707A VAL* 2.9 33.7 + - + +
710A ASP* 1.3 78.4 - - + +
712A SER* 1.3 60.2 + - - +
713A GLY 5.1 0.6 - - - -
572B GLU* 3.4 42.4 - - + +
573B TYR* 4.0 25.8 - - + -
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Residues in contact with SER 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535A ARG* 5.4 3.3 - - - +
625A HIS* 3.0 38.7 + - - -
646A ILE* 3.6 10.3 - - - +
708A ILE* 2.8 23.1 + - - +
709A GLU* 4.2 3.1 - - - -
710A ASP 3.3 0.2 - - - -
711A LEU* 1.3 78.7 - - - +
713A GLY* 1.3 65.1 + - - +
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Residues in contact with GLY 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709A GLU 3.1 15.5 + - - -
710A ASP 4.1 6.7 + - - -
711A LEU 3.7 1.1 - - - -
712A SER* 1.3 83.4 - - - +
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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