Contacts of the helix formed by residues 3546 - 3551 (chain D) in PDB entry 1PXX
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 LYS3546 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2044C ARG 5.0 5.3 + - - -
2046C GLU* 3.3 30.1 + - + +
2058C ASP* 3.6 13.6 + - - +
2060C THR* 3.7 32.3 + - + -
2061C ARG* 4.2 2.2 - - - +
2062C THR* 6.3 0.4 - - - +
3542D PRO 3.9 10.8 - - - -
3543D GLN* 3.4 31.5 + - - +
3544D TYR 2.9 6.7 + - - +
3545D TRP* 1.3 75.4 - - - +
3547D PRO* 1.3 78.1 - - + +
3548D SER* 3.8 16.4 - - - +
3549D THR* 3.0 26.9 + - - +
3550D PHE* 3.3 17.9 - - - -
3556D PHE* 4.0 4.9 - - - -
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Residues in contact with PRO3547 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2058C ASP* 3.4 15.0 - - - +
2060C THR* 3.8 9.9 - - + +
3546D LYS* 1.3 84.2 - - + -
3548D SER* 1.3 56.8 + - - +
3550D PHE* 2.8 16.5 + - - -
3552D GLY* 2.8 46.7 + - - +
3553D GLU* 3.0 35.0 - - + +
3556D PHE* 4.0 19.7 - - + -
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Residues in contact with SER3548 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2046C GLU* 3.2 31.0 + - - +
2047C CYS 5.6 0.4 - - - -
2048C MET* 4.0 32.8 - - - +
2058C ASP* 2.9 36.5 + - - +
3323D TRP* 5.6 1.4 - - - -
3546D LYS* 3.8 4.3 - - - +
3547D PRO* 1.3 73.4 - - - +
3549D THR* 1.3 63.6 + - - +
3550D PHE 3.3 0.7 + - - -
3551D GLY* 3.3 10.1 + - - -
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Residues in contact with THR3549 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2137C LYS* 3.0 34.7 + - + +
3331D THR* 3.9 8.8 - - - +
3334D LEU* 3.6 35.4 - - + +
3544D TYR* 2.8 45.1 + - + +
3546D LYS* 3.0 10.3 + - - +
3547D PRO 3.0 0.2 + - - -
3548D SER* 1.3 77.9 + - - +
3550D PHE* 1.3 69.5 + - + +
3551D GLY 3.5 1.3 + - - -
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Residues in contact with PHE3550 (chain D).
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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3316D LEU* 4.3 1.2 - - - +
3331D THR* 3.6 12.1 - - - +
3334D LEU* 4.1 24.9 - - + -
3335D ILE* 3.7 12.0 - - + +
3539D ILE* 4.4 15.7 - - + -
3544D TYR 3.8 17.0 - - - -
3545D TRP* 3.9 20.0 - + - -
3546D LYS 3.3 16.2 - - - -
3547D PRO 2.8 2.7 + - - +
3549D THR* 1.3 91.5 - - + +
3551D GLY* 1.3 57.0 + - - +
3552D GLY 3.3 1.6 - - - -
3555D GLY* 3.1 27.0 - - - -
3556D PHE* 2.9 57.2 - + - +
3559D ILE* 3.7 19.7 - - + -
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Residues in contact with GLY3551 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2048C MET* 3.9 5.5 - - - +
3316D LEU* 4.7 5.5 - - - +
3319D GLU* 5.3 2.6 - - - +
3320D HIS* 3.0 22.4 + - - -
3323D TRP* 3.6 29.6 - - - -
3331D THR* 3.6 4.9 - - - +
3547D PRO 3.3 0.4 + - - -
3548D SER 3.3 9.3 + - - -
3549D THR 3.5 1.4 - - - -
3550D PHE* 1.3 77.5 - - - +
3552D GLY* 1.3 58.0 + - - +
3554D VAL* 4.9 4.2 + - - +
3555D GLY 4.6 4.0 + - - -
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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