Contacts of the helix formed by residues 4359 - 4367 (chain B) in PDB entry 6W4H
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 ASP4359 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4280B TYR* 2.7 23.7 + - - -
4284B LEU* 3.2 31.4 - - - +
4290B PRO* 3.6 16.3 - - + +
4291B ILE 4.4 2.1 + - - +
4356B CYS 3.1 9.3 + - - +
4358B ASN* 1.3 88.9 + - - +
4360B PRO* 1.4 63.6 - - - +
4361B VAL* 3.8 2.9 + - - +
4362B GLY* 3.0 19.6 + - - -
4363B PHE* 3.0 20.6 + - - +
4366B LYS* 4.9 2.4 + - - -
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Residues in contact with PRO4360 (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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4291B ILE 4.9 1.1 - - - +
4294B CYS* 3.9 11.4 - - + -
4321B PHE* 3.7 26.5 - - + -
4326B CYS* 3.6 25.6 - - - -
4352B ILE* 4.0 20.0 - - + -
4356B CYS 4.1 0.2 - - - -
4357B ALA 3.4 16.8 - - - +
4358B ASN 3.7 2.5 - - - -
4359B ASP* 1.4 89.2 - - - +
4361B VAL* 1.3 62.4 + - - +
4363B PHE* 3.3 3.3 + - + +
4364B THR* 3.0 30.6 + - - +
4403B BDF 3.9 12.3 - - - -
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Residues in contact with VAL4361 (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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4280B TYR* 3.9 8.3 - - + +
4291B ILE* 3.9 27.1 - - + +
4294B CYS* 3.9 19.1 - - - -
4325B SER 4.2 2.5 - - - +
4326B CYS* 3.5 25.1 - - - +
4328B LEU* 3.8 46.2 - - + +
4331B ARG* 4.8 2.9 - - + -
4359B ASP* 3.3 5.9 - - - +
4360B PRO* 1.3 76.1 - - - +
4362B GLY* 1.3 61.3 - - - +
4364B THR* 2.8 17.8 + - - -
4365B LEU* 3.1 12.3 + - + +
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Residues in contact with GLY4362 (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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4280B TYR* 3.6 15.1 - - - -
4284B LEU* 4.4 4.7 - - - -
4359B ASP* 3.0 28.4 + - - -
4361B VAL* 1.3 75.3 - - - +
4363B PHE* 1.3 57.7 + - - +
4365B LEU* 3.4 3.7 + - - +
4366B LYS* 2.9 43.4 + - - +
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Residues in contact with PHE4363 (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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4352B ILE* 3.7 26.7 - - + -
4353B PRO* 3.4 33.7 - - + -
4356B CYS* 3.7 23.6 - - + -
4359B ASP 3.0 16.9 + - - +
4360B PRO 3.7 4.5 - - - +
4361B VAL 3.3 0.4 - - - -
4362B GLY* 1.3 76.3 - - - +
4364B THR* 1.3 59.7 + - - +
4366B LYS* 4.9 1.8 - - - -
4367B ASN* 2.9 59.7 + - + +
4376B TRP* 3.5 37.5 - + - -
4379B TYR* 3.6 32.3 - + - -
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Residues in contact with THR4364 (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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4326B CYS* 3.3 22.7 + - + +
4327B CYS* 5.2 0.5 - - - -
4328B LEU 5.4 0.5 + - - -
4345B LEU* 4.3 17.7 - - + +
4350B VAL* 3.8 29.8 - - + -
4352B ILE* 4.0 6.7 - - + -
4360B PRO 3.0 12.8 + - - +
4361B VAL 2.8 18.2 + - - -
4363B PHE* 1.3 75.1 - - - +
4365B LEU* 1.3 63.3 + - - +
4367B ASN 3.3 16.3 - - - +
4376B TRP* 4.1 16.7 - - + -
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Residues in contact with LEU4365 (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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4277B ALA* 4.5 12.6 - - + +
4280B TYR* 3.7 28.7 - - + -
4281B LYS* 4.1 23.5 + - + -
4328B LEU* 3.6 42.4 - - + +
4329B TYR* 4.1 24.9 - - + +
4361B VAL* 3.1 15.7 + - + +
4362B GLY* 3.7 4.3 - - - +
4363B PHE 3.3 0.2 - - - -
4364B THR* 1.3 86.0 + - - +
4366B LYS* 1.3 61.0 + - + +
4367B ASN 3.6 2.9 + - - +
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Residues in contact with LYS4366 (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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4281B LYS* 4.3 34.3 - - + +
4284B LEU* 3.8 32.3 - - - +
4359B ASP* 4.9 2.6 + - - -
4362B GLY* 2.9 23.9 + - - +
4363B PHE* 5.3 0.9 - - - -
4365B LEU* 1.3 76.2 - - + +
4367B ASN* 1.3 71.5 + - - +
4368B THR* 5.3 0.7 + - - -
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Residues in contact with ASN4367 (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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4363B PHE* 2.9 59.0 + - + +
4364B THR 3.3 13.9 - - - +
4365B LEU 3.3 2.8 - - - +
4366B LYS* 1.3 89.7 - - - +
4368B THR* 1.3 65.3 + - - +
4376B TRP* 3.6 24.1 - - + -
4377B LYS 4.3 7.0 - - - +
4379B TYR* 3.4 20.7 + - - -
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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