Contacts of the strand formed by residues 123 - 127 (chain G) in PDB entry 4WFH
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 SER 123 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121G PRO 3.9 1.7 + - - -
122G PRO* 1.3 71.4 - - - +
124G VAL* 1.3 61.1 + - - +
125G TYR* 3.4 36.9 + - - -
144G LEU 3.5 1.6 - - - +
145G VAL* 3.4 4.0 - - - -
146G LYS* 2.8 41.0 + - - +
147G GLY 4.9 0.2 + - - -
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Residues in contact with VAL 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F GLU* 5.3 3.3 - - - +
122G PRO* 3.9 18.8 + - + +
123G SER* 1.3 78.4 - - - +
125G TYR* 1.3 71.2 + - - +
126G PRO* 4.5 2.3 - - - +
143G CYS* 4.2 22.7 - - + -
144G LEU 3.3 7.2 - - - +
145G VAL* 4.5 16.8 - - + -
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Residues in contact with TYR 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F SER* 3.5 23.3 - - - +
122F GLU* 4.0 13.9 - - + -
123F GLN* 3.5 40.6 - - + +
126F SER* 3.6 17.3 + - - -
123G SER* 3.4 34.6 + - - -
124G VAL* 1.3 82.9 - - - +
126G PRO* 1.3 68.0 - - - +
127G LEU* 5.6 0.9 - - + -
143G CYS* 3.6 1.9 - - - -
144G LEU* 2.8 61.9 + - + +
146G LYS* 4.0 16.8 - - + -
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Residues in contact with PRO 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F PRO 5.2 0.9 - - - +
120F SER* 3.7 27.3 + - - -
122F GLU* 3.7 29.6 - - - +
124G VAL 4.3 2.0 - - - +
125G TYR* 1.3 88.7 - - - +
127G LEU* 1.3 68.3 + - - +
128G ALA* 3.9 5.2 + - + +
142G GLY 3.9 5.2 - - - +
143G CYS* 4.5 7.8 - - - -
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Residues in contact with LEU 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F PHE* 3.5 33.4 - - + +
118F PRO 4.7 8.1 - - - +
120F SER 5.7 2.0 - - - +
130F SER 5.4 3.6 - - - +
132F VAL* 4.0 29.6 - - + -
134F PHE* 3.9 26.9 - - + -
125G TYR* 5.2 1.1 - - + -
126G PRO* 1.3 80.8 - - - +
128G ALA* 1.3 60.4 + - - +
141G LEU* 3.7 6.8 - - - +
142G GLY* 2.8 45.6 + - - +
143G CYS 4.0 1.8 - - - +
144G LEU* 4.0 28.0 - - + +
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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