Contacts of the helix formed by residues 56 - 60 (chain B) in PDB entry 4PHZ
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 TRP 56 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ASP* 3.3 27.3 + - - -
53B TRP 3.9 2.8 + - - +
54B ASP 3.4 2.4 - - - -
55B PHE* 1.3 111.6 - + + +
57B VAL* 1.3 56.5 + - - +
58B ASP* 3.3 16.6 - - - +
59B TRP* 2.8 49.0 + + + +
60B LYS* 3.6 9.7 + - - +
113B PHE* 4.0 16.2 - + - -
119B PHE* 4.9 6.1 - + - -
123B LEU* 3.3 20.4 - - + -
124B VAL* 3.7 18.8 - - + -
195B ARG* 3.5 29.4 - - + -
198B MET* 3.4 18.8 - - + +
130C GLY 4.9 1.6 - - - -
134C MET* 3.6 38.3 - - + +
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Residues in contact with VAL 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A LEU* 4.1 3.1 - - - +
55B PHE 4.3 0.2 - - - -
56B TRP* 1.3 71.1 - - - +
58B ASP* 1.3 59.6 + - - +
60B LYS* 3.2 28.9 + - - +
122B SER 3.1 28.5 - - - +
123B LEU* 2.7 29.5 + - + +
125B PHE* 3.9 22.2 - - + -
169B ILE* 4.7 7.6 - - + -
172B PHE* 4.2 13.5 - - + -
173B HIS* 5.3 1.9 + - - +
186B ALA* 4.0 32.3 - - + +
189B ILE* 4.4 8.3 - - + -
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Residues in contact with ASP 58 (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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260A LEU* 3.9 11.1 - - - +
56B TRP* 3.3 8.8 - - - +
57B VAL* 1.3 74.3 - - - +
59B TRP* 1.3 61.9 + - - +
60B LYS 3.5 0.2 - - - -
123B LEU* 4.4 1.2 - - - +
186B ALA 3.6 21.3 - - - +
187B ASP* 4.4 4.4 - - - +
190B GLY* 4.0 8.2 - - - -
195B ARG* 2.7 45.6 + - - -
198B MET* 5.3 0.3 - - - +
203B ARG* 3.0 46.0 + - - +
205B VAL* 4.0 2.6 - - - +
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Residues in contact with TRP 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASP* 3.1 46.0 - - - -
53B TRP* 3.7 50.9 - + + -
56B TRP* 2.8 34.6 + + + +
58B ASP* 1.3 83.5 + - - +
60B LYS* 1.3 50.7 - - - +
61B ASP* 2.6 31.5 + - - +
65B TRP* 3.8 0.3 - - - +
198B MET* 3.4 40.0 - - + -
202B ILE* 3.6 22.4 - - + -
203B ARG* 2.8 39.4 - - + +
204B MET* 4.3 7.0 - - + -
205B VAL* 3.7 11.4 - - + +
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Residues in contact with LYS 60 (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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260A LEU* 3.4 14.5 - - - +
53B TRP 3.1 19.4 + - - +
54B ASP* 2.6 34.2 + - - +
56B TRP 3.6 13.7 - - - +
57B VAL* 3.2 21.3 + - - +
58B ASP 3.5 0.4 - - - -
59B TRP* 1.3 75.4 - - - +
61B ASP* 1.3 62.8 + - - +
65B TRP* 3.4 47.5 - - + +
125B PHE* 3.2 33.0 + - - -
126B PRO 4.6 3.1 - - - -
127B SER* 4.3 4.6 + - - -
162B TYR* 4.9 1.2 + - - -
169B ILE* 3.9 17.2 - - + +
173B HIS* 3.9 11.3 + - - -
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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