Contacts of the helix formed by residues 139 - 151 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A PHE* 4.0 7.2 - + - -
132A ASN 3.6 14.5 + - - -
133A LEU* 3.7 8.8 - - - +
134A CYS* 3.1 50.7 + - + -
137A THR* 3.0 15.0 + - - -
138A GLY* 1.3 81.6 - - - +
140A ALA* 1.3 62.8 + - - +
141A PRO* 3.5 2.5 - - - -
142A ILE* 3.1 11.8 + - + +
143A LEU* 3.0 17.2 + - - +
669B VAL* 4.8 7.4 - - + -
698B ILE* 5.3 0.9 - - - +
699B PRO* 2.7 35.5 + - + -
700B ALA* 3.8 11.2 - - - -
701B PHE* 3.3 57.9 - + + +
704B ARG* 4.5 7.9 - - + -
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Residues in contact with ALA 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A GLY 2.6 14.0 + - - +
139A TYR* 1.3 70.6 - - - +
141A PRO* 1.4 63.9 - - + +
143A LEU* 2.8 27.0 + - - +
144A ARG* 3.1 27.2 + - - +
665B GLU* 3.2 17.3 - - - +
704B ARG* 4.5 12.5 - - - +
708B PHE* 4.2 19.3 - - + -
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Residues in contact with PRO 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A HIS* 3.4 25.9 - - - +
99A HIS* 3.6 13.5 - - + +
100A GLY* 4.1 3.1 - - - -
102A GLN* 5.8 0.9 - - - +
137A THR* 3.7 37.5 - - + +
140A ALA* 1.4 93.2 - - + +
142A ILE* 1.3 57.0 + - - +
144A ARG* 3.1 19.8 + - + +
145A ALA* 3.1 26.9 + - - +
662B GLY* 6.3 1.8 - - - -
665B GLU* 3.5 16.8 - - - +
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Residues in contact with ILE 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A MET* 4.0 8.5 - - + -
100A GLY* 3.4 24.2 - - - +
106A CYS* 5.3 0.4 - - - -
110A PHE* 3.8 47.1 - - + -
114A MET* 4.2 11.8 - - - +
129A LEU* 4.0 9.4 - - + -
134A CYS* 4.6 5.2 - - + -
137A THR* 3.6 21.5 - - - +
139A TYR* 3.1 13.4 + - + +
140A ALA 3.1 1.4 + - - -
141A PRO* 1.3 74.3 - - - +
143A LEU* 1.3 63.7 + - - +
145A ALA* 3.4 6.9 - - - +
146A ALA* 3.0 21.7 + - - +
701B PHE* 3.7 17.5 - - + -
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Residues in contact with LEU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A TYR* 3.5 33.2 - - + -
139A TYR 3.0 9.7 + - - +
140A ALA* 2.8 18.5 + - - +
142A ILE* 1.3 68.9 - - - +
144A ARG* 1.3 64.9 + - + +
146A ALA* 3.3 3.2 + - - +
147A GLU* 3.1 44.2 + - - +
701B PHE* 4.1 20.4 - - + -
704B ARG* 4.0 26.9 - - - +
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Residues in contact with ARG 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A HIS* 3.6 31.8 + - + +
140A ALA* 3.1 14.6 + - - +
141A PRO* 3.1 42.4 - - - +
143A LEU* 1.3 72.5 - - + +
145A ALA* 1.3 56.7 + - - +
147A GLU* 3.1 14.8 + - - +
148A ALA* 2.7 38.3 + - - +
661B ILE* 6.0 1.2 - - - +
665B GLU* 3.3 23.8 + - - -
708B PHE* 4.9 10.5 + - - +
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Residues in contact with ALA 145 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A VAL 5.2 0.2 - - - +
94A ALA* 3.4 10.4 - - + +
95A MET* 3.8 43.5 - - + +
98A HIS* 4.1 7.0 - - + +
114A MET* 5.1 2.7 - - - -
141A PRO 3.1 11.3 + - - +
142A ILE 3.4 10.5 - - - +
144A ARG* 1.3 78.2 - - - +
146A ALA* 1.3 62.4 + - - +
148A ALA* 3.4 5.0 + - - +
149A ALA* 3.0 26.7 + - - +
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Residues in contact with ALA 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A VAL* 6.0 1.8 - - - -
114A MET* 5.0 16.8 - - + -
118A HIS* 5.9 0.2 - - - -
125A TYR* 3.7 38.6 + - + -
129A LEU* 5.3 3.1 - - + -
142A ILE 3.0 13.4 + - - +
143A LEU* 3.6 9.2 - - - +
144A ARG 3.1 0.2 - - - -
145A ALA* 1.3 75.1 - - - +
147A GLU* 1.3 64.5 + - - +
149A ALA* 3.1 6.9 + - - +
150A ALA* 3.0 23.4 + - - +
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Residues in contact with GLU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A TYR* 4.0 11.1 - - + -
143A LEU* 3.1 45.6 + - + +
144A ARG* 3.1 15.3 + - - +
146A ALA* 1.3 74.9 - - - +
148A ALA* 1.3 64.8 + - - +
150A ALA* 3.1 21.9 + - - +
151A GLY 3.9 2.6 + - - -
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Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ALA* 4.4 7.0 - - + -
98A HIS* 3.7 28.7 - - + +
144A ARG 2.7 19.7 + - - +
145A ALA* 3.4 6.3 - - - +
147A GLU* 1.3 73.1 - - - +
149A ALA* 1.3 59.3 + - - +
150A ALA 3.5 0.2 + - - -
151A GLY* 3.8 8.8 + - - -
152A GLU* 4.7 7.6 - - - +
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Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A PRO* 3.6 31.9 - - + +
91A VAL* 3.8 15.9 - - + +
94A ALA* 3.8 4.5 - - + -
118A HIS* 3.0 23.2 + - + -
145A ALA 3.0 16.7 + - - +
146A ALA* 3.1 4.0 + - - +
148A ALA* 1.3 73.6 - - - +
150A ALA* 1.3 59.3 + - - +
151A GLY 3.2 3.6 - - - -
152A GLU* 3.0 23.1 + - - +
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Residues in contact with ALA 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A HIS* 4.2 10.4 + - - -
123A LYS* 4.6 23.9 + - + +
125A TYR* 3.6 17.0 - - - +
146A ALA 3.0 12.3 + - - +
147A GLU* 3.1 13.6 + - - +
149A ALA* 1.3 75.0 - - - +
151A GLY* 1.3 62.8 + - - +
152A GLU 3.4 6.5 + - - +
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Residues in contact with GLY 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A GLU 3.9 2.4 + - - -
148A ALA 3.8 8.2 + - - -
149A ALA 3.2 1.6 - - - -
150A ALA* 1.3 79.5 - - - +
152A GLU* 1.3 64.2 + - - +
153A PRO* 3.8 1.9 - - - +
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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