Contacts of the helix formed by residues 4301 - 4312 (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 ARG4301 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4170A CYS* 6.0 4.0 - - - -
4174A ASN* 5.8 4.9 - - - +
4177A ALA* 4.6 2.2 - - - -
4299A GLY 3.5 0.6 - - - -
4300A ILE* 1.3 92.4 - - + +
4302A ARG* 1.3 65.7 + - - +
4303A GLU* 3.3 31.6 + - - +
4304A GLU* 3.5 32.0 + - + +
4305A PHE* 3.1 18.5 + - - -
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Residues in contact with ARG4302 (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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4161A PHE* 3.0 40.8 + - + +
4162A SER* 5.1 1.0 - - - +
4164A ILE* 3.9 9.3 + - - +
4166A VAL* 4.0 29.4 - - - +
4169A ILE* 3.5 40.8 - - + +
4170A CYS* 3.9 25.4 - - - -
4177A ALA* 4.4 7.8 - - + +
4301A ARG* 1.3 74.8 - - - +
4303A GLU* 1.3 63.9 + - - +
4305A PHE* 3.4 12.8 + - - +
4306A VAL* 3.3 41.9 + - + +
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Residues in contact with GLU4303 (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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4301A ARG* 3.3 26.0 + - - +
4302A ARG* 1.3 79.0 - - - +
4304A GLU* 1.3 61.3 - - + +
4306A VAL* 3.2 9.1 + - + +
4307A GLN* 2.9 49.8 + - + +
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Residues in contact with GLU4304 (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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4297A PRO* 5.3 2.2 - - + +
4299A GLY* 3.7 32.3 - - - -
4300A ILE 4.8 0.4 - - - +
4301A ARG* 3.5 32.9 + - + +
4302A ARG 3.3 0.4 - - - -
4303A GLU* 1.3 77.7 - - - +
4305A PHE* 1.3 57.7 + - - +
4307A GLN* 3.2 26.0 + - - +
4308A TRP* 2.9 28.7 + - - +
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Residues in contact with PHE4305 (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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4161A PHE* 4.8 17.5 - + + -
4169A ILE* 6.1 0.4 - - + -
4177A ALA* 3.8 9.4 - - + -
4178A ARG* 3.5 52.5 - - + -
4181A PHE* 4.1 22.2 - + + -
4297A PRO* 3.8 27.4 - - + -
4299A GLY 3.1 18.8 - - - -
4300A ILE* 3.4 22.2 - - - -
4301A ARG 3.1 20.1 + - - -
4302A ARG* 3.4 10.9 + - - +
4303A GLU 3.3 0.2 - - - -
4304A GLU* 1.3 79.9 - - - +
4306A VAL* 1.3 56.6 + - + +
4308A TRP* 3.2 8.5 + - - +
4309A VAL* 2.9 34.9 + - - +
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Residues in contact with VAL4306 (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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4158A LEU* 5.3 9.0 - - + -
4161A PHE* 4.7 22.0 - - + -
4302A ARG* 3.3 38.6 + - + +
4303A GLU* 3.2 12.4 + - + +
4305A PHE* 1.3 80.6 - - + +
4307A GLN* 1.3 57.6 + - + +
4309A VAL* 3.2 10.2 + - - +
4310A GLU* 2.9 48.8 + - + +
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Residues in contact with GLN4307 (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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4303A GLU* 2.9 39.7 + - + +
4304A GLU* 3.2 30.9 + - - +
4306A VAL* 1.3 76.6 - - + +
4308A TRP* 1.3 57.5 + - - +
4310A GLU* 3.2 16.9 + - - +
4311A LEU* 2.9 41.2 + - + +
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Residues in contact with TRP4308 (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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4157A MET* 5.8 1.1 - - + -
4181A PHE* 3.6 34.5 - + - -
4185A TRP* 4.9 8.1 - + - -
4284A LEU* 4.6 7.9 - - + -
4294A ILE* 4.1 15.0 - - + -
4295A GLN* 3.3 36.5 + - - +
4296A MET 4.9 0.2 - - - -
4297A PRO* 3.7 34.8 - - + +
4304A GLU 2.9 12.3 + - - +
4305A PHE 3.3 8.3 - - - +
4307A GLN* 1.3 75.1 - - - +
4309A VAL* 1.3 84.2 - - + +
4311A LEU* 3.2 24.0 + - + +
4312A LEU* 3.3 49.4 + - + +
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Residues in contact with VAL4309 (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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4154A LYS* 3.5 21.7 - - + +
4157A MET* 3.8 27.8 - - + -
4158A LEU* 3.8 34.5 - - + +
4161A PHE* 4.6 8.1 - - + -
4181A PHE* 4.6 4.3 - - + -
4305A PHE 2.9 20.0 + - - +
4306A VAL* 3.2 11.0 + - - +
4308A TRP* 1.3 90.2 - - + +
4310A GLU* 1.3 63.2 + - - +
4312A LEU* 3.2 28.0 + - + +
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Residues in contact with GLU4310 (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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4154A LYS* 3.2 26.3 + - - +
4158A LEU* 4.8 13.0 - - + +
4306A VAL* 2.9 38.5 + - + +
4307A GLN* 3.2 16.3 + - - +
4309A VAL* 1.3 76.0 - - - +
4311A LEU* 1.3 63.1 + - + +
4312A LEU 3.8 1.0 - - - +
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Residues in contact with LEU4311 (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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4307A GLN* 2.9 28.3 + - + +
4308A TRP* 3.2 17.7 + - + +
4310A GLU* 1.3 74.6 - - + +
4312A LEU* 1.3 63.1 + - - +
4313A PRO* 3.9 0.7 - - - +
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Residues in contact with LEU4312 (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* 6.0 0.2 - - + -
4154A LYS* 3.7 39.9 + - + -
4157A MET* 5.8 4.7 - - + -
4185A TRP* 5.8 1.6 - - + -
4294A ILE* 5.4 4.3 - - + -
4308A TRP* 3.3 54.2 + - + +
4309A VAL* 3.2 27.4 + - + +
4310A GLU 3.2 0.7 - - - +
4311A LEU* 1.3 81.1 - - - +
4313A PRO* 1.4 80.9 - - + +
4314A ASP* 3.8 2.3 + - - +
4320A TRP* 4.2 21.3 - - + -
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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