Contacts of the helix formed by residues 625 - 637 (chain C) in PDB entry 4JUO
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 LYS 625 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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620C VAL 4.7 1.6 - - - +
623C GLY 3.2 2.3 - - - -
624C ASP* 1.3 76.7 - - - +
626C VAL* 1.3 65.4 + - - +
628C PRO* 3.5 30.3 - - + +
629C ARG* 3.9 18.7 + - - +
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Residues in contact with VAL 626 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A GLY* 4.4 19.3 - - - +
624C ASP 3.6 6.7 + - - +
625C LYS* 1.3 72.8 - - - +
627C GLU* 1.3 60.3 + - - +
629C ARG* 3.4 22.5 + - + +
630C ARG* 2.8 49.8 + - - +
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Residues in contact with GLU 627 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626C VAL* 1.3 75.9 - - - +
628C PRO* 1.3 73.3 - - + +
630C ARG* 3.3 20.1 + - - +
631C LYS* 3.0 24.8 + - - +
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Residues in contact with PRO 628 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620C VAL* 4.1 25.2 - - + +
625C LYS* 3.5 30.5 - - + +
626C VAL 3.4 3.4 - - - -
627C GLU* 1.3 96.0 - - + +
629C ARG* 1.3 52.2 + - - +
631C LYS* 3.1 7.2 + - + +
632C TRP* 2.8 32.1 + - - +
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Residues in contact with ARG 629 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PHE* 3.9 24.0 - - + -
172A ALA* 5.5 0.9 - - - +
173A GLY* 4.7 13.2 - - - +
464C LYS* 3.7 20.2 - - - +
620C VAL 3.6 16.2 + - - +
621C LEU* 3.0 25.1 + - + +
622C MET 3.4 2.2 - - - -
623C GLY* 2.4 47.3 + - - +
624C ASP 4.9 0.6 + - - -
625C LYS 3.9 13.5 + - - +
626C VAL* 3.4 26.9 + - - +
628C PRO* 1.3 75.1 - - - +
630C ARG* 1.3 68.1 + - - +
632C TRP* 3.0 9.7 + - - +
633C ILE* 2.8 41.3 + - + +
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Residues in contact with ARG 630 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A GLY* 3.2 31.2 + - - +
174A TYR* 3.8 38.9 + - + +
626C VAL* 2.8 28.0 + - - +
627C GLU* 3.3 26.2 + - - +
629C ARG* 1.3 74.2 - - - +
631C LYS* 1.3 52.6 + - - +
633C ILE* 3.3 13.2 + - - +
634C GLU* 2.8 33.7 + - + +
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Residues in contact with LYS 631 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627C GLU 3.0 12.8 + - - +
628C PRO* 3.4 9.2 - - + +
630C ARG* 1.3 74.3 - - - +
632C TRP* 1.3 61.0 + - - +
633C ILE 3.1 1.1 - - - -
634C GLU* 3.6 7.5 - - + -
635C ASP* 2.7 68.3 + - + +
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Residues in contact with TRP 632 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLY* 3.6 29.2 - - - -
17A PHE* 4.9 1.3 - + - -
18A GLY* 4.3 20.6 - - - -
617C ARG* 3.6 42.7 - - - +
620C VAL* 4.2 18.6 - - + -
621C LEU* 3.7 29.7 - - + +
628C PRO 2.8 12.6 + - - +
629C ARG* 3.4 12.3 - - - +
631C LYS* 1.3 79.0 - - - +
633C ILE* 1.3 69.1 + - + +
635C ASP* 4.7 1.1 - - - -
636C ASN* 2.8 70.7 + - + +
637C VAL* 4.5 5.8 - - + -
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Residues in contact with ILE 633 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PHE* 4.3 6.3 - - + -
21A SER* 4.2 23.6 - - - -
25A ILE* 4.4 10.3 - - + -
172A ALA 4.4 16.6 - - - +
173A GLY* 4.5 2.5 - - - -
174A TYR* 5.4 6.5 - - + +
629C ARG* 2.8 41.1 + - + +
630C ARG* 3.5 10.1 - - - +
632C TRP* 1.3 87.0 - - + +
634C GLU* 1.3 67.5 + - - +
635C ASP 2.9 0.2 + - - -
637C VAL* 2.8 50.2 + - + +
639C PHE* 3.9 18.2 - - + -
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Residues in contact with GLU 634 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A TYR* 4.9 9.8 + - - +
630C ARG* 2.8 21.9 + - + +
631C LYS* 3.7 9.9 - - + +
633C ILE* 1.3 75.9 - - - +
635C ASP* 1.3 63.2 + - - +
637C VAL 4.5 6.1 - - - +
639C PHE* 5.1 8.0 - - - -
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Residues in contact with ASP 635 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631C LYS* 2.7 47.1 + - + +
632C TRP* 4.0 2.9 - - - +
634C GLU* 1.3 79.1 - - - +
636C ASN* 1.3 69.7 + - - +
637C VAL 3.7 0.8 - - - -
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Residues in contact with ASN 636 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617C ARG* 5.7 1.4 + - - -
632C TRP* 2.8 81.6 + - + +
635C ASP* 1.3 80.6 - - - +
637C VAL* 1.3 63.2 + - - +
638C LYS* 3.6 4.5 + - - +
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Residues in contact with VAL 637 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLY* 3.8 31.9 - - - +
21A SER* 4.9 1.1 - - - -
22A LYS* 4.0 20.0 - - + -
632C TRP* 4.5 6.3 - - + -
633C ILE* 2.8 37.4 + - + +
634C GLU 4.5 5.0 - - - +
635C ASP 3.7 0.4 - - - -
636C ASN* 1.3 76.8 - - - +
638C LYS* 1.3 59.6 + - - +
639C PHE* 3.2 49.6 + - + -
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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