Contacts of the helix formed by residues 3556 - 3568 (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 GLU3556 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3554A ARG* 2.9 25.5 + - + +
3555A LEU* 1.3 75.9 - - - +
3557A ALA* 1.3 60.3 + - - +
3558A THR* 3.1 17.8 + - - +
3559A GLN* 2.8 32.9 + - + +
3560A LEU* 2.8 33.8 + - - +
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Residues in contact with ALA3557 (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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3556A GLU* 1.3 73.4 - - - +
3558A THR* 1.3 62.7 + - + +
3560A LEU* 3.4 15.5 + - + +
3561A GLU* 3.1 28.7 + - - +
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Residues in contact with THR3558 (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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3556A GLU* 3.5 22.9 + - - +
3557A ALA* 1.3 75.3 - - + +
3559A GLN* 1.3 69.5 + - - -
3561A GLU* 3.3 23.3 + - + +
3562A GLY* 3.3 5.2 + - - -
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Residues in contact with GLN3559 (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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3553A MET* 3.4 29.8 - - + +
3554A ARG 3.3 22.7 - - - +
3555A LEU* 4.6 2.9 - - - -
3556A GLU* 2.8 41.6 + - + +
3558A THR* 1.3 80.2 + - - +
3560A LEU* 1.3 52.4 + - + +
3562A GLY* 3.0 4.6 + - - -
3563A VAL* 2.8 38.6 + - + +
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Residues in contact with LEU3560 (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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3555A LEU* 4.0 27.1 - - + -
3556A GLU 2.8 30.9 + - - +
3557A ALA* 3.6 14.6 - - + +
3559A GLN* 1.3 73.3 - - - +
3561A GLU* 1.3 60.2 + - - +
3563A VAL* 3.6 8.0 - - + +
3564A ALA* 2.8 30.8 + - - +
3629A PHE* 4.8 4.0 - - + -
3634A PHE* 3.6 62.8 - - + -
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Residues in contact with GLU3561 (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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3557A ALA 3.1 17.5 + - - +
3558A THR* 3.3 13.2 - - - +
3559A GLN 3.1 0.2 - - - -
3560A LEU* 1.3 79.5 - - - +
3562A GLY* 1.3 58.0 + - - +
3564A ALA* 3.2 7.4 + - - +
3565A ARG* 2.9 56.4 + - - +
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Residues in contact with GLY3562 (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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3558A THR 3.3 5.5 + - - -
3559A GLN* 3.0 7.8 + - - -
3561A GLU* 1.3 78.6 - - - +
3563A VAL* 1.3 61.9 + - - +
3565A ARG* 3.3 18.1 + - - +
3566A ARG* 3.3 19.9 + - - +
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Residues in contact with VAL3563 (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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3553A MET* 4.0 27.1 - - + -
3559A GLN* 2.8 28.2 + - + +
3560A LEU* 3.6 11.2 - - + +
3562A GLY* 1.3 73.3 - - - +
3564A ALA* 1.3 50.9 + - - +
3566A ARG* 3.1 21.5 + - + +
3567A MET* 2.8 61.6 + - + +
3627A GLN* 4.5 4.9 - - - +
3629A PHE* 4.4 19.7 - - + -
3634A PHE* 4.2 10.8 - - + -
3660A VAL* 5.2 3.8 - - + -
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Residues in contact with ALA3564 (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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3560A LEU 2.8 21.2 + - - +
3561A GLU* 3.2 10.5 + - - +
3563A VAL* 1.3 71.9 - - - +
3565A ARG* 1.3 66.9 + - - +
3567A MET* 3.5 12.9 - - - +
3568A THR* 2.8 33.5 + - - -
3638A HIS* 4.3 18.6 - - + +
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Residues in contact with ARG3565 (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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3561A GLU* 2.9 43.0 + - - +
3562A GLY* 3.4 14.4 - - - +
3563A VAL 3.2 0.2 - - - -
3564A ALA* 1.3 84.5 - - - +
3566A ARG* 1.3 56.8 + - - +
3568A THR* 3.1 25.6 - - - +
3569A VAL* 3.6 9.5 - - - +
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Residues in contact with ARG3566 (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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3553A MET* 3.6 15.0 - - - +
3562A GLY 3.4 8.2 + - - +
3563A VAL* 3.1 28.9 - - + +
3565A ARG* 1.3 75.6 - - - +
3567A MET* 1.3 62.8 + - + +
3568A THR 3.4 0.7 - - - -
3569A VAL* 3.4 23.2 - - - +
3572A ASP* 4.5 11.0 - - + +
3573A TYR* 3.5 19.1 + - + +
3625A VAL* 5.8 0.4 - - - +
3627A GLN* 3.5 22.2 + - - +
3660A VAL* 6.2 1.3 - - + -
3662A ALA* 3.6 28.7 - - - +
3664A VAL* 4.2 17.0 + - - -
2518B TYR* 2.8 28.5 + - - -
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Residues in contact with MET3567 (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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3528A SER* 4.9 0.2 + - - -
3563A VAL* 2.8 47.5 + - + +
3564A ALA* 3.0 7.6 + - - +
3566A ARG* 1.3 76.8 - - + +
3568A THR* 1.3 58.6 + - - +
3569A VAL 3.1 5.8 + - - -
3570A GLU* 4.0 6.6 - - - +
3573A TYR* 3.1 48.0 + - + +
3575A LEU* 3.7 28.0 - - + -
3634A PHE* 4.4 9.4 - - + -
3638A HIS* 3.6 37.9 - - + +
3642A LEU* 3.8 14.2 - - + +
3658A MET* 5.3 1.6 - - + -
3660A VAL* 5.0 4.0 - - + -
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Residues in contact with THR3568 (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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3564A ALA 2.8 12.1 + - - +
3565A ARG* 3.1 26.9 - - + +
3567A MET* 1.3 76.8 - - - +
3569A VAL* 1.3 65.2 + - + +
3570A GLU* 3.6 7.5 + - - +
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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