Contacts of the helix formed by residues 3584 - 3599 (chain A) in PDB entry 2RT5
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 ASP3584 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3582A GLY 4.3 0.2 - - - -
3583A ARG* 1.3 118.7 + - + +
3585A GLN* 1.3 56.9 + - - +
3586A GLU* 3.0 37.6 + - - +
3587A ASP* 3.0 4.9 + - - +
3588A VAL* 2.8 37.9 + - - +
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Residues in contact with GLN3585 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3584A ASP* 1.3 75.0 - - - +
3586A GLU* 1.3 63.3 + - - +
3588A VAL* 3.3 10.1 + - - +
3589A VAL* 3.1 33.2 + - + +
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Residues in contact with GLU3586 (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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3583A ARG* 4.1 15.8 + - - -
3584A ASP* 3.0 11.0 + - - +
3585A GLN* 1.3 78.6 - - - +
3587A ASP* 1.3 70.9 + - - +
3589A VAL* 3.1 12.4 + - + +
3590A SER* 3.1 27.4 + - - -
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Residues in contact with ASP3587 (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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3581A CYS 4.2 3.1 - - - +
3582A GLY* 3.2 7.2 - - - -
3583A ARG* 2.8 43.4 + - + +
3584A ASP* 3.0 22.5 + - - +
3586A GLU* 1.3 86.0 - - - +
3588A VAL* 1.3 57.3 + - - +
3590A SER* 3.1 7.7 + - - -
3591A GLN* 2.9 46.5 + - - +
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Residues in contact with VAL3588 (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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3580A PRO* 4.0 16.3 - - + +
3582A GLY* 3.4 31.2 - - - +
3584A ASP 2.8 23.9 + - - +
3585A GLN* 3.4 10.5 - - + +
3587A ASP* 1.3 75.7 - - - +
3589A VAL* 1.3 55.3 + - + +
3591A GLN* 3.3 4.0 + - - +
3592A THR* 2.7 45.8 + - - +
3653A ILE* 5.7 4.3 - - + -
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Residues in contact with VAL3589 (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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3585A GLN* 3.1 25.5 + - + +
3586A GLU* 3.1 12.1 + - + +
3588A VAL* 1.3 77.4 - - + +
3590A SER* 1.3 58.4 + - - +
3592A THR* 3.2 7.5 + - - -
3593A GLU* 2.8 32.9 + - + +
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Residues in contact with SER3590 (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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3586A GLU* 3.1 22.8 + - - -
3587A ASP* 3.5 12.6 - - - -
3589A VAL* 1.3 77.6 - - - +
3591A GLN* 1.3 61.1 + - - +
3593A GLU* 3.3 7.6 + - - +
3594A SER* 2.9 37.1 + - - -
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Residues in contact with GLN3591 (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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3512A LEU* 5.3 1.9 - - - +
3519A THR* 4.4 4.2 + - - -
3520A ALA* 3.6 10.8 - - - +
3521A ALA* 2.9 39.9 - - + +
3580A PRO* 3.9 17.7 - - + +
3581A CYS 4.0 18.6 - - - +
3587A ASP* 2.9 34.5 + - - +
3588A VAL* 3.7 5.4 - - - +
3590A SER* 1.3 79.7 + - - +
3592A THR* 1.3 56.5 + - - +
3594A SER* 3.4 5.2 + - - -
3595A LEU* 2.8 31.9 + - - +
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Residues in contact with THR3592 (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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3580A PRO* 3.4 21.8 - - + +
3588A VAL* 2.7 31.5 + - - +
3589A VAL* 3.4 7.8 - - - -
3591A GLN* 1.3 76.9 - - - +
3593A GLU* 1.3 56.9 + - - +
3595A LEU* 3.3 3.2 + - - +
3596A LYS* 2.8 43.9 + - + +
3653A ILE* 4.1 11.8 - - + +
3655A PRO* 3.9 32.3 - - + +
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Residues in contact with GLU3593 (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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3589A VAL* 2.8 22.6 + - + +
3590A SER* 3.4 9.4 - - - +
3592A THR* 1.3 77.4 - - - +
3594A SER* 1.3 64.9 + - - +
3596A LYS* 3.4 24.0 + - - +
3597A ALA* 3.2 25.3 + - - +
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Residues in contact with SER3594 (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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3518A ASP* 6.4 0.7 - - - -
3519A THR 3.9 19.7 - - - -
3520A ALA* 4.9 1.1 - - - -
3590A SER* 2.9 23.0 + - - -
3591A GLN* 3.8 8.7 + - - -
3593A GLU* 1.3 76.7 - - - +
3595A LEU* 1.3 58.5 + - - +
3597A ALA* 3.3 4.9 + - - +
3598A ALA* 2.8 36.4 + - - +
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Residues in contact with LEU3595 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3513A LEU* 4.9 0.4 - - + -
3520A ALA* 3.5 25.1 - - + +
3522A VAL* 4.0 15.5 - - + -
3578A ALA 5.0 1.6 - - - +
3580A PRO* 3.9 29.2 - - + -
3591A GLN 2.8 18.4 + - - +
3592A THR 3.3 4.5 + - - +
3594A SER* 1.3 76.7 - - - +
3596A LYS* 1.3 57.0 + - + +
3599A PHE* 2.8 57.5 + - + +
3600A ILE* 2.9 18.3 + - + +
3655A PRO 4.1 11.7 - - - +
3656A HIS* 4.4 9.2 - - - -
3657A LEU* 3.7 14.6 - - + -
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Residues in contact with LYS3596 (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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3592A THR* 2.8 28.0 + - + +
3593A GLU* 3.7 27.1 + - - +
3595A LEU* 1.3 75.3 - - - +
3597A ALA* 1.3 54.6 + - + +
3600A ILE* 3.1 14.9 - - + +
3601A THR* 2.6 41.8 + - - +
3655A PRO* 3.5 35.7 - - + +
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Residues in contact with ALA3597 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3593A GLU* 3.2 18.7 + - - +
3594A SER* 3.9 3.6 - - - +
3596A LYS* 1.3 79.3 - - - +
3598A ALA* 1.3 64.2 + - + +
3601A THR* 3.5 20.9 - - - +
3602A TYR* 4.2 2.6 + - - +
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Residues in contact with ALA3598 (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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3515A LEU* 3.5 11.0 - - + +
3516A LYS* 5.9 0.2 - - - -
3518A ASP* 3.4 38.8 - - + +
3519A THR 5.6 0.7 - - - +
3594A SER* 2.8 19.4 + - - +
3597A ALA* 1.3 79.9 - - + +
3599A PHE* 1.3 71.0 + - + +
3602A TYR* 3.1 23.6 - - - +
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Residues in contact with PHE3599 (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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3513A LEU* 3.2 48.2 - - + -
3514A ALA* 3.3 8.5 - - - -
3515A LEU* 3.4 27.4 - - + -
3518A ASP 3.3 20.6 - - - -
3520A ALA* 4.1 11.7 - - + -
3549A ILE* 3.5 24.2 - - + -
3595A LEU* 2.8 36.5 + - + -
3598A ALA* 1.3 82.3 - - + +
3600A ILE* 1.3 56.2 + - - +
3601A THR 3.5 0.2 - - - -
3602A TYR 3.9 0.2 - - - -
3603A LEU* 2.8 41.9 + - + +
3657A LEU* 3.9 22.9 - - + -
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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