Contacts of the helix formed by residues 199 - 203 (chain J) 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 PRO 199 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84I PHE* 3.7 22.2 - - + -
139I ASN* 3.7 20.2 - - + +
197J SER 3.6 7.4 - - - +
198J MET* 1.4 91.1 - - - +
200J GLU* 1.3 67.6 + - - +
201J TYR* 2.8 48.0 + - + +
202J ILE* 3.1 31.3 + - + +
203J ARG* 4.4 0.7 + - - +
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Residues in contact with GLU 200 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84I PHE* 3.4 33.4 - - + -
107I PRO 4.0 4.3 - - - +
108I ARG* 3.5 22.0 - - + +
109I SER* 3.3 25.9 + - - +
262I ALA* 3.5 1.2 - - - -
263I GLY 3.3 22.9 + - - +
198J MET* 3.6 3.3 + - - -
199J PRO* 1.3 71.4 - - - +
201J TYR* 1.3 63.1 + - - +
202J ILE 3.3 0.9 + - - -
203J ARG* 2.9 49.6 + - - +
207J ARG* 3.1 18.2 + - - -
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Residues in contact with TYR 201 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E GLN* 5.7 3.2 + - - +
82I VAL* 3.6 34.1 - - + -
83I SER 4.0 15.0 - - - -
84I PHE* 4.1 0.7 - - + -
109I SER* 3.7 9.8 - - - +
139I ASN* 3.4 31.5 - - - +
140I VAL 3.1 20.6 + - - -
141I GLU* 3.3 44.2 - - + +
144I GLY* 5.0 1.6 + - - -
199J PRO* 2.8 30.6 + - + +
200J GLU* 1.3 82.7 + - - +
202J ILE* 1.3 92.8 + - + +
203J ARG 3.3 1.2 + - - -
204J MET 4.7 0.3 + - - -
207J ARG* 3.3 17.9 + - - +
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Residues in contact with ILE 202 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B ARG* 5.8 5.6 - - - +
141I GLU* 5.2 0.9 - - - -
59J TRP* 3.5 28.4 - - + -
197J SER 4.8 5.8 - - - +
198J MET* 3.6 20.4 - - + -
199J PRO* 3.1 26.4 + - + +
201J TYR* 1.3 94.9 - - + +
203J ARG* 1.3 65.4 + - - +
204J MET* 3.3 11.9 + - - +
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Residues in contact with ARG 203 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108I ARG* 4.8 0.4 - - - +
260I LEU* 3.4 18.0 - - - +
261I GLN 3.3 16.3 + - - -
262I ALA* 3.6 8.6 - - - +
58J ASP* 3.0 38.7 + - - +
59J TRP* 2.7 55.8 - - + +
187J ASP* 2.6 28.0 + - - -
198J MET* 5.5 2.0 - - + -
199J PRO 5.1 0.9 - - - +
200J GLU* 2.9 54.9 + - - +
201J TYR 3.2 2.6 - - - -
202J ILE* 1.3 77.9 - - + +
204J MET* 1.3 62.2 + - - +
205J VAL* 3.9 15.5 - - + +
207J ARG* 3.8 6.1 - - - +
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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