Contacts of the helix formed by residues 499 - 505 (chain D) in PDB entry 4S15
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 LEU 499 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A GLU* 4.2 15.2 + - + +
332A GLN* 4.1 34.5 - - + +
333A TYR* 3.7 16.5 + - + +
505B PRO* 4.2 12.1 - - + -
506B LEU* 4.0 34.3 - - + +
509B GLU* 3.0 15.1 + - - +
498D THR* 1.3 79.2 - - - +
500D LEU* 1.3 58.8 + - - +
502D LEU* 3.1 26.2 + - + +
503D LEU* 2.9 37.9 + - + +
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Residues in contact with LEU 500 (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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335B VAL* 4.6 13.9 - - + -
353B ILE* 4.1 36.1 - - + -
356B LEU* 4.3 21.5 - - + -
357B LYS* 5.0 4.0 - - + -
506B LEU* 4.0 21.9 - - + +
509B GLU* 3.0 22.3 + - + +
510B LEU* 3.8 26.7 - - + -
498D THR* 5.5 0.2 - - - -
499D LEU* 1.3 76.9 - - - +
501D GLN* 1.3 61.7 + - + +
503D LEU* 3.3 4.9 + - + +
504D LEU* 3.0 40.8 + - + +
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Residues in contact with GLN 501 (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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349B GLN* 4.9 9.7 + - - -
353B ILE* 4.4 16.6 - - + +
498D THR* 2.4 43.6 + - - +
500D LEU* 1.3 79.1 - - + +
502D LEU* 1.3 61.3 + - - +
504D LEU* 3.4 0.7 + - - -
505D GLY 3.1 3.5 + - - -
506D HIS* 2.9 59.1 + - + +
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Residues in contact with LEU 502 (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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286A GLU 4.9 4.0 - - - +
287A THR* 4.6 9.6 - - + -
332A GLN* 3.9 17.9 - - + +
333A TYR* 3.6 51.1 - - + -
336A GLU* 3.8 32.8 - - + -
340A ARG* 4.2 15.1 + - - +
498D THR 2.9 12.6 + - - +
499D LEU* 3.1 20.4 + - + +
501D GLN* 1.3 77.2 - - - +
503D LEU* 1.3 65.9 + - + +
505D GLY* 3.1 14.3 + - - -
506D HIS 5.4 1.6 - - - -
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Residues in contact with LEU 503 (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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332A GLN* 4.0 23.6 - - - +
336A GLU* 5.4 10.9 - - + +
332B GLN* 5.8 5.6 - - + +
335B VAL* 4.4 22.0 - - + -
336B GLU* 4.6 7.4 - - - +
339B LYS* 2.8 30.9 + - - +
506B LEU* 4.0 33.9 - - + -
503C LEU* 4.4 16.4 - - + -
499D LEU* 2.9 31.3 + - + +
500D LEU* 3.7 6.3 - - + +
502D LEU* 1.3 82.2 - - + +
504D LEU* 1.3 61.1 + - - +
505D GLY 3.6 0.2 + - - -
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Residues in contact with LEU 504 (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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335B VAL* 4.3 4.9 - - + -
339B LYS* 3.8 28.0 - - + -
344B PHE* 4.3 5.2 - - + -
345B MET* 3.3 25.5 - - - +
352B GLN* 3.9 14.6 - - + +
353B ILE* 4.0 17.3 - - + -
356B LEU* 3.9 31.0 - - + -
500D LEU* 3.0 26.3 + - + +
501D GLN 4.0 1.3 - - - +
503D LEU* 1.3 77.4 - - - +
505D GLY* 1.3 62.1 + - - +
506D HIS* 3.5 40.1 + - + +
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Residues in contact with GLY 505 (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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340A ARG* 4.2 16.8 + - - -
501D GLN 3.1 3.4 + - - -
502D LEU* 3.1 12.2 + - - -
503D LEU 3.3 1.0 + - - -
504D LEU* 1.3 79.8 - - - +
506D HIS* 1.3 65.5 + - - +
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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