Contacts of the helix formed by residues 3530 - 3538 (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 ASN3530 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3528A SER 4.0 0.4 + - - -
3529A GLY* 1.3 71.4 - - - -
3531A ASN* 1.3 65.3 + - - +
3532A VAL* 2.8 41.3 + - - +
3533A LEU* 3.1 26.9 + - + +
3571A THR* 3.9 34.9 + - - +
3573A TYR 3.0 7.7 + - - -
3574A CYS* 3.0 19.8 - - - -
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Residues in contact with ASN3531 (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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3508A VAL* 4.8 9.3 - - + +
3526A PHE* 3.5 37.5 - - + -
3529A GLY 3.7 1.6 + - - -
3530A ASN* 1.3 76.4 + - - +
3532A VAL* 1.3 77.7 + - - +
3534A ALA* 3.1 15.0 + - - +
3535A HIS* 3.3 11.3 + - - +
3574A CYS* 4.1 1.1 - - - -
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Residues in contact with VAL3532 (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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3530A ASN* 2.8 19.8 + - - +
3531A ASN* 1.3 88.5 - - - +
3533A LEU* 1.3 65.0 + - - +
3535A HIS* 3.2 12.6 + - + +
3536A ARG* 2.9 39.6 + - + +
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Residues in contact with LEU3533 (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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3530A ASN* 3.1 22.1 + - + +
3532A VAL* 1.3 78.3 - - - +
3534A ALA* 1.3 50.4 + - - +
3536A ARG* 3.1 19.1 - - - +
3537A SER* 2.6 37.4 + - - -
3571A THR 3.5 18.8 - - - +
3572A ASP 3.6 8.5 - - - +
3573A TYR* 3.3 36.1 - - - +
3574A CYS* 3.6 7.9 - - + +
3624A TYR* 3.9 20.2 - - + +
3661A ILE* 3.9 11.3 - - + +
3663A SER* 3.1 21.8 - - - +
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Residues in contact with ALA3534 (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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3508A VAL* 3.8 20.6 - - + -
3530A ASN 3.9 0.8 + - - -
3531A ASN 3.1 10.5 + - - +
3533A LEU* 1.3 77.8 - - - +
3535A HIS* 1.3 59.0 + - - +
3538A LEU* 2.8 56.8 + - + +
3574A CYS* 4.0 2.9 - - - -
3576A LEU* 3.8 8.7 - - + -
3661A ILE* 3.3 20.8 - - + +
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Residues in contact with HIS3535 (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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3508A VAL* 5.4 9.1 + - + +
3531A ASN* 3.3 8.0 + - - +
3532A VAL* 3.2 16.5 + - + +
3534A ALA* 1.3 79.1 - - - +
3536A ARG* 1.3 61.3 + - + +
3538A LEU* 3.9 12.1 - - - +
3540A LEU* 5.3 8.6 - - + +
3617A PRO* 5.3 3.3 - - - +
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Residues in contact with ARG3536 (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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3532A VAL* 2.9 29.9 + - + +
3533A LEU* 3.1 32.7 - - - +
3535A HIS* 1.3 79.4 - - + +
3537A SER* 1.3 59.9 + - - +
3538A LEU 5.1 0.2 - - - -
3615A PRO 4.2 0.7 - - - +
3616A ASN* 3.0 34.1 + - - +
3617A PRO* 3.1 32.8 - - + +
3624A TYR* 3.0 32.0 + - + +
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Residues in contact with SER3537 (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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3533A LEU 2.6 22.8 + - - -
3534A ALA 3.2 3.5 + - - -
3536A ARG* 1.3 80.2 - - - +
3538A LEU* 1.3 64.0 + - - +
3539A PRO* 3.1 15.1 - - - +
3614A VAL* 3.2 40.4 - - - +
3615A PRO 4.8 2.3 - - - +
3624A TYR* 4.5 8.5 - - - -
3626A LEU* 4.0 4.4 - - - +
3661A ILE* 3.2 32.2 - - - +
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Residues in contact with LEU3538 (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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3508A VAL* 3.7 5.4 - - + +
3509A TRP* 3.3 40.0 - - + +
3524A LEU* 4.1 12.3 - - + -
3534A ALA* 2.8 44.8 + - + +
3535A HIS* 3.9 10.5 - - - +
3536A ARG 5.2 0.2 - - - -
3537A SER* 1.3 74.0 - - - +
3539A PRO* 1.3 69.8 - - - +
3540A LEU* 3.5 14.0 - - - +
3547A LEU* 3.6 18.2 - - + -
3576A LEU* 3.7 13.0 - - + -
3626A LEU* 3.4 30.5 - - + -
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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