Contacts of the helix formed by residues 3548 - 3554 (chain B) in PDB entry 5NUG
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 ALA3548 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3547B ILE* 1.3 82.0 - - - +
3549B ARG* 1.3 66.0 + - - +
3550B THR* 4.4 5.6 - - + +
3551B GLU* 4.0 33.7 + - + +
3552B TYR* 3.6 19.6 + - - +
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Residues in contact with ARG3549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3510B SER* 4.8 3.9 + - - +
3513B PHE* 3.4 44.2 - - + -
3522B GLN* 5.2 5.7 - - - +
3525B ARG* 5.9 0.4 - - - +
3526B GLN* 4.6 25.5 - - - +
3529B PHE* 3.6 53.2 - - + +
3547B ILE 3.9 1.2 + - - +
3548B ALA* 1.3 74.6 - - - +
3550B THR* 1.3 63.0 + - - +
3552B TYR* 3.4 4.6 + - - +
3553B LEU* 3.4 34.3 + - + +
3571B ASP* 4.8 7.1 + - - -
3575B GLU* 3.2 31.0 + - + +
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Residues in contact with THR3550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3548B ALA* 4.8 5.4 - - + -
3549B ARG* 1.3 79.5 - - - +
3551B GLU* 1.3 75.4 + - + +
3553B LEU* 4.3 1.1 - - - +
3554B SER* 3.2 27.2 + - - -
3559B ARG* 4.2 6.0 + - - -
3571B ASP* 4.8 12.1 - - + +
3574B THR* 2.4 50.2 - - + +
3575B GLU* 4.7 14.1 - - - -
3578B ILE* 3.9 9.6 - - - +
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Residues in contact with GLU3551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3547B ILE* 5.8 2.6 - - + +
3548B ALA* 4.0 25.9 + - + +
3549B ARG 3.4 0.6 - - - -
3550B THR* 1.3 83.4 - - + +
3552B TYR* 1.3 65.2 + - - +
3554B SER 3.2 12.6 - - - +
3559B ARG* 4.3 25.6 + - - +
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Residues in contact with TYR3552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3186B LEU* 5.6 1.8 - - + -
3190B LYS* 2.7 75.6 + - + +
3194B LEU* 5.9 2.7 - - + +
3503B ILE* 4.4 5.2 - - - +
3506B ASP* 3.1 45.6 + - + +
3507B CYS* 3.8 14.2 - - - -
3510B SER* 4.0 22.9 - - - -
3544B ARG* 5.0 8.5 - - - -
3547B ILE* 3.9 19.6 - - + +
3548B ALA 3.6 17.4 + - - +
3549B ARG* 3.4 5.5 + - - +
3550B THR 3.3 0.2 - - - -
3551B GLU* 1.3 81.7 - - - +
3553B LEU* 1.3 60.0 + - + +
3554B SER 4.3 1.4 - - - +
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Residues in contact with LEU3553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3186B LEU* 3.8 29.2 - - + -
3190B LYS* 3.5 9.3 + - - +
3510B SER* 3.1 30.5 - - - +
3513B PHE* 5.8 3.6 - - + -
3514B ILE* 3.6 26.0 - - + -
3549B ARG* 3.4 23.3 + - + +
3550B THR* 4.3 2.2 - - - +
3551B GLU 3.5 0.2 - - - -
3552B TYR* 1.3 86.8 - - + +
3554B SER* 1.3 62.4 + - - +
3555B ASN* 4.0 2.4 + - - +
3578B ILE* 3.7 22.4 - - + -
3581B LYS* 5.5 0.5 + - - -
3582B ARG* 3.3 39.0 + - - +
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Residues in contact with SER3554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3550B THR 3.2 14.9 + - - -
3551B GLU 3.2 19.4 - - - +
3552B TYR 4.3 0.9 - - - +
3553B LEU* 1.3 80.5 - - - +
3555B ASN* 1.3 75.2 + - - +
3558B GLU* 3.8 11.1 + - - +
3559B ARG* 3.4 21.8 + - - +
3562B TRP* 3.4 14.1 - - - -
3578B ILE* 3.6 21.3 - - - -
3582B ARG* 4.6 2.7 - - - +
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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