Contacts of the helix formed by residues 141 - 148 (chain C) in PDB entry 2W4G
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 ALA 141 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138C ASN 3.0 0.2 + - - -
140C GLU 1.3 3.6 - - - +
142C PHE 1.3 6.1 - - - -
144C LYS* 3.5 0.5 - - - +
145C HIS* 2.6 12.8 + - + -
733M PRO* 0.6 118.6 + - - +
734M GLU* 0.9 173.4 + - + +
735M GLY 2.1 2.0 - - - +
737M PHE* 2.5 43.3 - - + +
738M MET* 2.3 14.1 - - - -
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Residues in contact with PHE 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C GLN* 3.3 38.6 - - + -
137C ILE* 3.2 13.0 - - + -
138C ASN 3.2 0.7 - - - -
141C ALA* 1.3 8.5 - - - +
143C VAL 1.3 24.9 - - - -
146C ILE* 3.1 2.0 - - + +
732M ILE* 1.2 179.1 + - + +
733M PRO* 0.5 301.6 + - + +
734M GLU 1.8 1.6 - - - +
735M GLY 2.7 3.7 - - - +
736M GLN* 0.5 222.8 - - + -
737M PHE* 3.4 9.2 - - + -
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Residues in contact with VAL 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C PHE* 4.6 10.5 - - + -
87C PHE* 4.3 4.7 - - + -
88C VAL* 3.7 17.5 - - + -
140C GLU 4.4 1.1 - - - +
142C PHE* 1.3 60.8 - - - +
144C LYS* 1.3 58.4 + - + +
147C MET* 2.8 50.9 + - + +
730M SER 2.6 3.6 - - - +
731M ALA* 0.4 192.3 + - + +
732M ILE 1.7 22.0 + - - +
733M PRO* 2.5 4.5 - - - -
734M GLU 3.1 0.2 - - - +
735M GLY 4.1 1.6 - - - +
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Residues in contact with LYS 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C PHE* 5.9 2.9 - - + -
140C GLU* 4.5 0.6 - - - +
141C ALA 3.5 1.6 - - - +
143C VAL* 1.3 70.3 - - + +
145C HIS* 1.3 57.0 + - + +
147C MET* 3.7 3.5 - - - +
148C SER* 2.9 31.5 + - - -
733M PRO* 2.3 7.6 - - - +
734M GLU* 0.7 269.9 + - + +
738M MET* 5.4 0.2 - - - -
742M LYS* 3.7 22.2 - - - +
746M LYS* 2.2 37.4 - - - +
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Residues in contact with HIS 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C GLN* 2.7 33.4 + - + +
141C ALA* 2.6 11.7 + - + -
144C LYS* 1.3 50.0 - - + +
146C ILE* 1.3 58.1 + - + -
148C SER* 3.0 21.7 + - - +
733M PRO* 1.3 96.7 - - + +
734M GLU* 5.8 0.7 - - + -
737M PHE* 3.7 33.5 - + - -
797M PHE* 3.2 19.8 - - - -
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Residues in contact with ILE 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C LEU* 5.1 17.3 - - + +
130C GLN* 6.0 2.2 - - - +
142C PHE* 3.1 7.6 - - + +
143C VAL 4.2 0.4 - - - +
145C HIS* 1.3 72.0 - - + +
147C MET* 1.3 63.2 + - - +
148C SER 3.1 0.7 + - - -
149C VAL* 4.7 0.2 - - - +
730M SER* 3.2 25.1 - - - +
732M ILE* 2.0 48.2 - - + -
733M PRO* 2.6 10.8 - - + +
793M ARG* 3.4 28.1 - - + -
794M CYS* 4.2 16.2 - - - +
797M PHE* 2.7 38.4 - - + +
800M ARG* 4.8 0.3 + - - -
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Residues in contact with MET 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C GLY 3.8 8.3 - - - +
84C PHE* 3.5 50.9 - - + -
87C PHE* 6.1 3.6 - - - -
143C VAL* 2.8 34.2 + - + +
144C LYS* 4.1 2.2 - - - +
146C ILE* 1.3 71.3 - - + +
148C SER* 1.3 54.8 + - - +
149C VAL 3.1 11.7 + - - +
730M SER* 5.3 1.8 - - - -
793M ARG* 1.4 93.3 + - - +
800M ARG* 5.0 3.0 + - - -
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Residues in contact with SER 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C LYS 2.9 17.0 + - - -
145C HIS* 3.0 26.7 + - - +
146C ILE 3.1 2.2 + - - -
147C MET* 1.3 73.4 - - - +
149C VAL* 1.3 60.4 + - - +
797M PHE* 4.4 1.7 - - - -
804M ARG* 5.0 4.3 + - - -
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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