Contacts of the helix formed by residues 630 - 638 (chain A) in PDB entry 5ON2
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 PRO 630 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU* 3.6 25.8 - - + +
49A HIS* 4.1 2.9 - - - -
50A MET* 3.8 23.6 - - + -
53A VAL* 3.7 22.2 - - + -
111A GLN* 5.0 3.4 - - + +
115A LEU* 4.7 9.0 - - + -
628A ILE 3.4 8.7 - - - +
629A ASP* 1.4 88.2 - - - +
631A GLN* 1.3 60.0 + - - +
632A VAL 3.2 0.4 - - - -
633A MET* 3.1 12.6 + - + +
634A VAL* 2.9 37.8 + - + +
642A VAL* 4.8 4.7 - - + -
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Residues in contact with GLN 631 (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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107A TYR* 5.3 6.3 - - - +
110A ASN* 5.2 1.3 + - - -
111A GLN* 3.6 38.0 + - - +
114A MET* 3.1 44.7 - - - +
115A LEU* 6.1 0.3 - - - +
629A ASP* 3.3 20.2 + - - +
630A PRO* 1.3 79.3 - - - +
632A VAL* 1.3 62.0 + - + +
634A VAL* 3.9 11.6 - - - +
635A GLU* 3.1 54.2 + - - +
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Residues in contact with VAL 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A ASP* 3.9 17.0 + - + +
630A PRO 3.1 0.8 + - - -
631A GLN* 1.3 78.9 - - + +
633A MET* 1.3 57.6 + - + +
635A GLU* 3.5 7.8 + - - +
636A ARG* 3.1 25.6 + - - +
608D ALA* 3.4 24.0 - - + +
609D GLY* 3.3 27.6 - - - +
610D HIS* 3.4 33.0 - - + +
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Residues in contact with MET 633 (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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50A MET* 4.6 7.4 - - + +
628A ILE* 5.4 4.7 - - - -
629A ASP 5.4 2.7 - - - +
630A PRO* 3.1 10.5 + - - +
632A VAL* 1.3 77.3 - - + +
634A VAL* 1.3 58.5 + - - +
636A ARG* 4.3 5.4 - - - -
637A TYR* 2.8 43.8 + - + +
638A GLY 3.5 2.9 + - - -
642A VAL* 3.7 31.2 - - + +
645A PHE* 4.6 2.9 - - + -
658A TRP* 4.0 24.2 - - + -
660A GLU* 3.6 31.4 - - - +
663A VAL* 3.4 30.1 - - + -
608D ALA 4.6 9.2 - - - +
609D GLY* 6.5 0.2 - - - -
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Residues in contact with VAL 634 (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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11A GLU* 5.1 2.6 - - - +
114A MET* 4.6 24.5 - - + +
115A LEU* 3.8 29.6 - - + -
630A PRO* 2.9 25.1 + - + +
631A GLN* 4.0 24.2 - - - +
633A MET* 1.3 76.6 - - - +
635A GLU* 1.3 59.8 + - - +
638A GLY* 2.9 31.8 + - - +
639A ALA* 4.1 15.3 - - + +
642A VAL* 4.1 11.7 - - + -
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Residues in contact with GLU 635 (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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8A GLU* 5.8 4.0 - - - +
114A MET* 5.1 7.4 - - + +
631A GLN* 3.1 48.8 + - - +
632A VAL* 3.9 6.6 - - - +
633A MET 3.4 0.2 - - - -
634A VAL* 1.3 75.2 - - - +
636A ARG* 1.3 62.6 + - - +
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Residues in contact with ARG 636 (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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7A PRO* 5.6 2.3 - - - +
632A VAL 3.1 17.5 + - - +
633A MET* 3.8 3.6 - - - +
635A GLU* 1.3 80.5 + - - +
637A TYR* 1.3 93.4 + - + +
605D LYS* 3.3 48.6 - - - +
609D GLY* 3.7 25.8 + - - +
611D GLU* 2.8 42.2 + - - +
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Residues in contact with TYR 637 (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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7A PRO* 3.4 19.1 - - - +
633A MET* 2.8 30.2 + - + +
636A ARG* 1.3 96.1 - - + +
638A GLY* 1.3 57.6 + - - +
641A THR* 3.0 35.5 + - + +
642A VAL* 5.2 2.2 - - + -
660A GLU* 4.9 6.7 - - - -
663A VAL* 4.0 26.9 - - + +
664A GLU* 2.9 31.2 + - - -
667A ASN* 3.8 29.5 + - + +
605D LYS* 3.3 21.7 + - - -
608D ALA 6.1 0.9 - - - -
609D GLY* 6.2 1.8 - - - -
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Residues in contact with GLY 638 (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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7A PRO* 4.1 9.6 - - - -
11A GLU* 3.8 13.2 - - - -
633A MET 3.5 0.8 + - - -
634A VAL* 2.9 22.4 + - - -
636A ARG 3.8 0.2 - - - -
637A TYR* 1.3 79.1 - - - +
639A ALA* 1.3 64.5 + - - -
640A ASP 3.4 2.7 - - - -
641A THR* 3.4 3.9 + - - -
642A VAL* 3.2 23.7 + - - +
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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