Contacts of the helix formed by residues 4327 - 4333 (chain D) in PDB entry 6W75
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 CYS4327 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4323D GLY 3.4 3.5 + - - +
4324D ALA 3.2 11.4 + - - +
4325D SER 3.5 0.6 - - - -
4326D CYS* 1.3 78.2 - - - +
4328D LEU* 1.3 61.8 + - - +
4329D TYR* 3.6 12.3 - - - -
4330D CYS* 3.4 9.6 - - + -
4331D ARG* 2.9 33.8 + - - +
4336D HIS* 3.5 9.0 - - - -
4343D CYS* 3.6 7.0 - - - -
4344D ASP* 5.5 0.7 - - - -
4345D LEU* 3.7 19.7 - - + -
4361D VAL* 4.5 0.2 - - - -
4364D THR* 5.0 0.4 - - - -
4401D ZN 2.3 36.6 - - - -
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Residues in contact with LEU4328 (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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4272B PHE* 4.1 3.1 - - + -
4276D ALA* 3.6 42.0 - - + +
4277D ALA* 3.7 5.6 - - - +
4280D TYR* 4.0 15.9 - - + -
4291D ILE* 3.8 18.6 - - + -
4326D CYS 3.9 0.4 + - - -
4327D CYS* 1.3 71.7 - - - +
4329D TYR* 1.3 60.5 + - + +
4331D ARG* 3.8 2.2 - - - -
4332D CYS* 2.8 63.9 + - + +
4361D VAL* 3.7 22.6 - - + +
4364D THR* 5.3 1.0 + - - -
4365D LEU* 3.6 32.5 - - + +
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Residues in contact with TYR4329 (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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4276D ALA* 4.4 12.1 - - + -
4277D ALA* 3.7 23.0 - - - +
4327D CYS* 3.2 11.4 - - - -
4328D LEU* 1.3 77.3 - - + +
4330D CYS* 1.3 64.9 + - - +
4333D HIS* 3.0 18.9 + - - -
4334D ILE* 3.0 45.6 + - + +
4335D ASP 3.4 16.8 - - - +
4336D HIS* 3.5 22.9 - + + +
4337D PRO* 3.5 39.2 - - + +
4365D LEU* 4.1 21.0 - - + +
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Residues in contact with CYS4330 (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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6902C VAL* 3.1 27.3 - - + +
4324D ALA* 3.5 23.8 - - - +
4327D CYS* 3.3 7.1 + - - +
4329D TYR* 1.3 77.1 - - - +
4331D ARG* 1.3 61.7 + - - +
4333D HIS* 3.2 15.8 + - - +
4336D HIS* 3.7 9.2 - - - -
4343D CYS* 3.9 6.1 - - - -
4346D LYS* 4.3 23.3 - - - -
4401D ZN 2.3 33.4 - - - -
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Residues in contact with ARG4331 (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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6874C LYS 4.2 14.8 + - - -
6875C GLY 5.1 1.0 + - - -
6876C VAL* 3.7 19.1 - - - +
6902C VAL* 4.1 11.0 - - - +
4291D ILE* 3.5 31.4 - - + +
4292D THR* 2.9 30.5 + - - +
4293D ASN* 3.9 16.3 + - - +
4294D CYS* 4.0 1.2 - - - +
4324D ALA 4.1 2.2 - - - +
4325D SER* 2.9 45.8 + - - +
4327D CYS 2.9 22.8 + - - +
4328D LEU* 3.9 4.3 - - - +
4330D CYS* 1.3 76.1 - - - +
4332D CYS* 1.3 58.6 + - - +
4333D HIS* 3.4 15.1 + - - -
4361D VAL* 4.7 1.6 - - + -
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Residues in contact with CYS4332 (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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4272B PHE* 3.7 24.0 - - - -
4274B VAL* 4.3 9.9 - - + -
4334B ILE* 6.0 0.5 - - - +
4335B ASP* 4.4 6.8 + - - +
4291D ILE* 4.7 5.4 - - - -
4328D LEU* 2.8 46.4 + - - +
4331D ARG* 1.3 73.6 - - - +
4333D HIS* 1.3 71.8 + - - +
4334D ILE* 3.5 25.9 + - + +
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Residues in contact with HIS4333 (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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4333B HIS 3.9 11.4 - - - +
4334B ILE* 4.5 5.2 - - - -
4335B ASP* 3.9 28.2 + - - +
6875C GLY* 5.2 1.8 + - - -
6900C ASP* 3.8 33.0 + - + -
6901C PHE* 4.5 8.3 - - - -
6902C VAL* 3.7 27.0 - - + +
4329D TYR 3.0 6.7 + - - -
4330D CYS 3.2 6.2 + - - -
4331D ARG 3.4 15.8 + - - -
4332D CYS* 1.3 81.1 - - - +
4334D ILE* 1.3 61.2 + - - +
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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