Contacts of the helix formed by residues 139 - 150 (chain C) in PDB entry 2W3S
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 TYR 139 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110C PHE* 3.9 6.3 - + - -
132C ASN 3.6 14.4 - - - -
133C LEU* 3.6 7.3 - - - +
134C CYS* 3.0 50.5 + - + -
137C THR* 3.0 13.5 + - - -
138C GLY* 1.3 81.3 - - - +
140C ALA* 1.3 61.7 + - - +
141C PRO* 3.4 3.1 - - - -
142C ILE* 2.9 19.9 + - + +
143C LEU* 3.0 11.8 + - - +
669D VAL* 4.8 6.5 - - + -
698D ILE* 5.2 0.2 - - - +
699D PRO* 2.9 29.1 + - + -
700D ALA* 3.5 24.3 - - - -
701D PHE* 3.3 42.4 - + + +
704D ARG* 4.1 18.6 - - + -
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Residues in contact with ALA 140 (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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138C GLY 2.6 15.1 + - - +
139C TYR* 1.3 71.4 - - - +
141C PRO* 1.4 68.5 - - + +
143C LEU* 3.3 7.0 + - - +
144C ARG* 3.1 34.0 + - - +
665D GLU* 3.5 18.8 - - - +
704D ARG* 4.1 12.5 - - - +
708D PHE* 4.1 22.0 - - + -
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Residues in contact with PRO 141 (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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98C HIS* 3.4 26.0 - - - +
99C HIS* 3.6 14.4 - - + +
100C GLY* 3.7 4.7 - - - -
137C THR* 3.5 41.7 - - + +
139C TYR 3.4 0.9 - - - -
140C ALA* 1.4 93.3 - - + +
142C ILE* 1.3 57.6 + - - +
144C ARG* 2.9 22.9 + - - +
145C ALA* 3.0 25.3 + - - +
662D GLY* 6.4 1.3 - - - -
665D GLU* 4.3 8.3 - - - +
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Residues in contact with ILE 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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95C MET* 4.1 5.8 - - + -
100C GLY* 3.5 26.0 - - - +
106C CYS* 5.6 0.9 - - - -
110C PHE* 3.6 56.3 - - + -
114C MET* 4.1 16.5 - - - +
129C LEU* 4.2 3.6 - - + -
134C CYS* 4.5 4.9 - - - -
137C THR* 3.7 22.0 - - - +
139C TYR* 2.9 13.5 + - - +
141C PRO* 1.3 71.2 - - - +
143C LEU* 1.3 66.3 + - - +
145C ALA* 3.1 7.6 + - - +
146C ALA* 2.9 22.5 + - - +
701D PHE* 3.8 9.2 - - + -
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Residues in contact with LEU 143 (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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125C TYR* 3.7 37.5 - - + -
139C TYR 3.0 10.2 + - - +
140C ALA* 3.6 12.1 - - - +
142C ILE* 1.3 76.4 - - - +
144C ARG* 1.3 61.8 + - + +
146C ALA* 3.3 2.1 + - - -
147C GLU* 3.1 47.4 + - + +
701D PHE* 4.0 12.5 - - + -
704D ARG* 3.5 35.2 - - - +
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Residues in contact with ARG 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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98C HIS* 3.5 30.7 + - + +
140C ALA* 3.1 17.9 + - - +
141C PRO* 2.9 41.2 - - - +
142C ILE 3.2 0.2 - - - -
143C LEU* 1.3 73.5 - - + +
145C ALA* 1.3 65.9 + - - +
147C GLU* 3.4 12.5 + - - +
148C ALA* 3.0 26.0 + - - +
661D ILE* 5.7 2.6 - - - +
665D GLU* 3.0 28.1 + - - -
708D PHE 4.8 9.9 + - - -
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Residues in contact with ALA 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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91C VAL* 6.2 0.2 - - - -
94C ALA* 3.4 14.1 - - + +
95C MET* 3.6 46.4 - - + +
98C HIS* 4.2 8.9 - - + -
100C GLY* 5.5 0.2 - - - -
114C MET* 4.9 2.0 - - - -
141C PRO 3.0 11.0 + - - +
142C ILE 3.1 8.0 + - - +
144C ARG* 1.3 77.0 - - - +
146C ALA* 1.3 62.1 + - - +
148C ALA 3.3 0.2 + - - -
149C ALA* 2.9 26.3 + - - +
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Residues in contact with ALA 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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91C VAL* 5.7 1.6 - - - -
114C MET* 4.8 17.6 - - + -
125C TYR* 3.3 47.4 + - + -
129C LEU* 5.2 3.1 - - + -
142C ILE 2.9 16.3 + - - +
143C LEU* 3.7 5.8 - - - +
145C ALA* 1.3 75.2 - - - +
147C GLU* 1.3 62.3 + - - +
149C ALA* 3.3 7.7 + - - +
150C ALA* 3.1 18.5 + - - -
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Residues in contact with GLU 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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125C TYR* 4.2 13.9 - - + -
143C LEU* 3.1 49.4 + - + +
144C ARG* 3.8 12.3 - - - +
146C ALA* 1.3 74.6 - - - +
148C ALA* 1.3 63.5 + - - +
150C ALA* 3.7 13.9 + - - +
151C GLY 4.1 2.3 + - - -
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Residues in contact with ALA 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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94C ALA* 4.8 4.5 - - + -
98C HIS* 3.6 24.7 - - + +
144C ARG 3.0 17.5 + - - +
145C ALA 3.8 2.7 - - - +
147C GLU* 1.3 75.0 - - - +
149C ALA* 1.3 65.2 + - - +
150C ALA 3.3 0.9 + - - -
151C GLY* 3.3 13.3 + - - -
152C GLU* 4.3 5.2 + - - +
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Residues in contact with ALA 149 (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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90C PRO* 4.0 17.5 - - - +
91C VAL* 3.8 33.2 - - + +
94C ALA* 4.1 3.5 - - + +
118C HIS* 2.9 23.4 + - + -
145C ALA 2.9 17.7 + - - +
146C ALA* 3.6 6.1 - - - +
148C ALA* 1.3 76.0 - - - +
150C ALA* 1.3 62.0 + - - +
152C GLU* 3.0 16.2 + - - +
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Residues in contact with ALA 150 (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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118C HIS* 4.3 10.2 + - - -
121C ASP* 5.2 5.0 - - - +
123C LYS* 4.2 24.9 + - + +
125C TYR* 3.7 14.6 - - - +
146C ALA 3.1 12.0 + - - +
147C GLU* 3.7 13.2 - - - +
148C ALA 3.2 0.6 - - - -
149C ALA* 1.3 73.4 - - - +
151C GLY* 1.3 67.0 + - - +
152C GLU 3.4 6.8 + - - +
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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