Contacts of the helix formed by residues 4317 - 4322 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4192A GLU* 3.5 13.9 - - - +
4196A TYR* 4.9 0.9 - - - -
4287A LYS* 3.3 21.7 + - - +
4288A VAL* 6.0 2.7 - - + -
4315A THR* 5.1 5.4 - - + +
4316A GLN* 1.3 80.7 - - - +
4318A PRO* 1.3 74.4 - - + +
4319A SER* 3.7 2.9 - - - -
4320A TRP* 3.2 28.7 + - - +
4325A ASN* 3.7 18.2 - - - +
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Residues in contact with PRO4318 (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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4192A GLU* 4.0 10.1 - - - +
4196A TYR* 3.9 28.7 - - + +
4317A THR* 1.3 83.5 - - + +
4319A SER* 1.3 56.0 + - - +
4320A TRP 3.1 5.6 - - - -
4321A LEU* 2.9 30.6 + - + +
4323A LEU* 3.6 13.7 - - + +
4324A PRO 3.9 19.5 - - - +
4325A ASN* 3.9 13.0 - - + +
4327A ALA* 5.9 0.7 - - + -
4328A GLU* 3.6 28.5 - - + +
4332A LEU* 6.0 2.5 - - + -
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Residues in contact with SER4319 (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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4285A ALA* 4.4 1.2 - - - +
4286A CYS* 2.9 27.7 + - - +
4287A LYS 3.1 21.6 + - - -
4288A VAL* 3.8 5.2 + - - -
4289A ASP 4.7 0.9 + - - -
4317A THR* 3.2 1.5 - - - -
4318A PRO* 1.3 76.7 - - - +
4320A TRP* 1.3 56.1 + - - +
4321A LEU 3.0 5.2 - - - -
4322A GLY* 3.0 19.0 + - - -
4323A LEU 3.5 14.9 + - - +
4325A ASN* 3.3 28.2 + - - -
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Residues in contact with TRP4320 (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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4153A VAL* 4.1 24.2 - - + -
4154A LYS* 5.5 2.9 - - + -
4185A TRP* 3.9 38.2 - + + -
4189A ILE* 4.9 0.9 - - - +
4192A GLU* 4.2 10.3 - - - +
4285A ALA* 3.1 24.9 - - - +
4287A LYS* 4.1 21.0 - - + +
4294A ILE* 3.9 22.2 - - + -
4308A TRP* 6.1 0.2 - + - -
4312A LEU* 4.2 20.6 - - + -
4313A PRO* 3.7 42.4 - - + -
4315A THR 5.1 1.0 + - - -
4316A GLN* 3.9 22.0 - - + +
4317A THR* 3.2 39.9 + - - +
4318A PRO 3.1 0.6 + - - -
4319A SER* 1.3 75.1 - - - +
4321A LEU* 1.3 59.0 + - + +
4322A GLY 3.4 1.3 - - - -
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Residues in contact with LEU4321 (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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4153A VAL* 5.2 0.2 - - + -
4189A ILE* 3.2 48.0 - - + +
4192A GLU* 3.2 38.6 - - + +
4193A ARG* 3.0 47.4 + - + +
4196A TYR* 4.0 4.7 - - + -
4268A PHE* 4.2 13.5 - - + -
4285A ALA* 5.3 0.7 - - - -
4318A PRO 2.9 11.1 + - - +
4320A TRP* 1.3 79.6 - - + +
4322A GLY* 1.3 59.0 + - - +
4323A LEU* 3.2 24.2 - - + -
4637A GLU* 4.3 6.6 - - - +
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Residues in contact with GLY4322 (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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4285A ALA* 4.8 5.6 - - - +
4286A CYS* 5.6 7.0 - - - -
4319A SER* 3.0 13.5 + - - -
4320A TRP 3.4 1.6 - - - -
4321A LEU* 1.3 76.6 - - - +
4323A LEU* 1.3 57.9 + - - +
4634A SER 4.4 0.6 - - - +
4637A GLU* 3.7 15.3 + - - +
4638A ARG* 3.1 38.0 + - - +
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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