Contacts of the helix formed by residues 4317 - 4322 (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 THR4317 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4192B GLU* 3.5 14.3 - - - +
4196B TYR* 4.9 0.9 - - - -
4287B LYS* 3.3 21.4 + - - +
4288B VAL* 6.0 2.5 - - + -
4315B THR* 5.1 5.8 - - + +
4316B GLN* 1.3 80.4 - - - +
4318B PRO* 1.3 75.0 - - + +
4319B SER* 3.7 2.8 - - - -
4320B TRP* 3.2 30.5 + - - +
4325B ASN* 3.7 18.4 - - - +
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Residues in contact with PRO4318 (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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4192B GLU* 4.0 10.5 - - - +
4196B TYR* 3.9 28.5 - - + +
4317B THR* 1.3 83.8 - - + +
4319B SER* 1.3 55.7 + - - +
4320B TRP 3.1 5.4 - - - -
4321B LEU* 2.9 31.3 + - + +
4323B LEU* 3.6 13.4 - - + +
4324B PRO 3.9 18.8 - - - +
4325B ASN* 3.9 13.2 - - + +
4327B ALA* 5.9 0.7 - - + -
4328B GLU* 3.6 27.8 - - + +
4332B LEU* 6.0 2.9 - - + -
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Residues in contact with SER4319 (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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4285B ALA* 4.4 1.2 - - - +
4286B CYS* 2.9 28.3 + - - +
4287B LYS 3.1 22.1 + - - -
4288B VAL* 3.8 5.2 + - - -
4289B ASP 4.7 1.0 + - - -
4317B THR* 3.2 0.9 - - - -
4318B PRO* 1.3 76.3 - - - +
4320B TRP* 1.3 55.4 + - - +
4321B LEU 3.0 5.6 - - - -
4322B GLY* 3.0 18.6 + - - -
4323B LEU 3.5 14.9 + - - +
4325B ASN* 3.3 28.3 + - - -
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Residues in contact with TRP4320 (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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4153B VAL* 4.1 24.7 - - + -
4154B LYS* 5.5 2.5 - - + -
4185B TRP* 3.9 38.6 - + + -
4189B ILE* 4.9 0.5 - - - +
4192B GLU* 4.2 9.9 - - - +
4285B ALA* 3.1 25.7 - - - +
4287B LYS* 4.1 20.4 - - + +
4294B ILE* 3.9 21.8 - - + -
4312B LEU* 4.2 20.2 - - + -
4313B PRO* 3.7 42.0 - - + -
4315B THR 5.1 1.0 + - - -
4316B GLN* 3.9 21.1 - - + +
4317B THR* 3.2 42.2 + - - +
4318B PRO 3.1 0.4 + - - -
4319B SER* 1.3 75.7 - - - +
4321B LEU* 1.3 58.7 + - + +
4322B GLY 3.4 1.1 - - - -
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Residues in contact with LEU4321 (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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4189B ILE* 3.2 47.8 - - + +
4192B GLU* 3.2 39.7 - - - +
4193B ARG* 3.0 45.9 + - + +
4196B TYR* 4.0 4.9 - - + -
4268B PHE* 4.2 13.2 - - + -
4285B ALA* 5.3 0.7 - - - -
4318B PRO 2.9 10.2 + - - +
4320B TRP* 1.3 80.0 - - + +
4322B GLY* 1.3 59.2 + - - +
4323B LEU* 3.2 23.8 - - + -
4637B GLU* 4.3 6.5 - - - +
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Residues in contact with GLY4322 (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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4285B ALA* 4.8 5.7 - - - +
4286B CYS* 5.6 6.7 - - - -
4319B SER* 3.0 13.3 + - - -
4320B TRP 3.4 1.6 + - - -
4321B LEU* 1.3 78.0 - - - +
4323B LEU* 1.3 57.5 + - - +
4634B SER 4.4 0.3 - - - +
4637B GLU* 4.1 14.7 + - - +
4638B ARG* 3.1 37.0 + - - +
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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