Contacts of the helix formed by residues 140 - 154 (chain B) in PDB entry 2YZ2
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 140 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A LYS* 5.9 4.9 - - - +
134B ARG* 5.0 0.8 - - - +
138B PHE 3.7 1.2 + - - -
139B LEU* 1.3 77.3 - - - +
141B GLY* 1.3 63.5 + - - +
142B GLY* 3.7 3.6 + - - -
143B GLU* 3.0 37.0 + - - +
144B LYS* 3.0 19.1 + - - +
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Residues in contact with GLY 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A THR* 5.0 16.9 - - - +
88B GLU* 5.7 2.1 - - - +
140B SER* 1.3 72.5 - - - +
142B GLY* 1.3 56.4 + - - +
144B LYS* 3.5 13.4 - - - +
145B ARG* 3.2 28.1 + - - +
169B LEU* 5.6 4.5 - - - +
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Residues in contact with GLY 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B SER* 3.2 3.8 + - - -
141B GLY* 1.3 72.8 - - - +
143B GLU* 1.3 62.9 + - - +
145B ARG* 3.4 8.0 + - - +
146B ARG* 3.1 30.0 + - - +
169B LEU* 6.6 0.2 - - - -
173B GLY* 6.0 6.7 - - - -
176B ASP* 4.8 3.3 - - - +
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Residues in contact with GLU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B LEU* 4.1 8.9 - - + +
131B PHE* 3.4 40.1 - - + -
134B ARG* 4.0 9.0 + - - -
139B LEU* 3.7 15.5 - - + +
140B SER* 3.0 38.7 + - - +
142B GLY* 1.3 72.1 - - - +
144B LYS* 1.3 59.9 + - - +
146B ARG* 3.5 12.5 - - - +
147B VAL* 3.0 33.4 + - - +
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Residues in contact with LYS 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B GLU* 4.0 36.9 + - + +
89B ASP* 5.1 3.0 + - - -
91B PHE* 3.3 23.9 - - + -
136B PRO 3.5 20.9 - - - +
137B PHE* 3.1 47.6 + - - +
139B LEU* 3.8 16.4 - - + +
140B SER 3.0 11.3 + - - +
141B GLY* 3.5 16.2 - - - +
142B GLY 3.3 0.2 - - - -
143B GLU* 1.3 74.5 - - - +
145B ARG* 1.3 57.8 + - - +
147B VAL* 3.1 4.0 + - - -
148B ALA* 2.9 26.6 + - - +
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Residues in contact with ARG 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B PHE 5.4 0.2 + - - -
86B TYR* 4.1 16.4 - - - +
87B PRO* 4.0 26.8 - - - +
88B GLU* 3.7 20.8 + - - +
141B GLY 3.2 14.3 + - - +
142B GLY* 3.6 7.4 - - - +
143B GLU 3.3 0.2 - - - -
144B LYS* 1.3 79.2 - - - +
146B ARG* 1.3 56.4 + - + +
148B ALA* 3.3 6.0 + - - +
149B ILE* 3.1 31.8 + - + +
165B PRO* 2.5 38.1 + - - +
167B VAL 3.6 18.2 + - - -
168B GLY 5.4 0.4 - - - -
169B LEU* 3.7 26.4 - - + +
173B GLY* 5.9 1.8 - - - +
177B LEU* 3.4 31.6 - - + +
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Residues in contact with ARG 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B VAL* 3.3 49.4 + - + +
125B GLY* 2.7 33.3 + - - -
126B LEU* 3.9 16.8 - - + +
142B GLY 3.1 18.6 + - - +
143B GLU* 3.5 13.4 - - - +
145B ARG* 1.3 73.2 - - - +
147B VAL* 1.4 58.8 + - - +
149B ILE* 3.5 3.3 + - - -
150B ALA* 2.9 23.9 + - - +
176B ASP* 2.7 42.3 + - - +
179B ARG* 3.5 8.0 - - - +
180B ILE* 5.4 3.6 - - + -
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Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B PHE* 3.8 21.8 - - + -
96B VAL* 3.9 17.5 - - + -
99B GLU* 4.0 18.6 - - + -
100B VAL* 4.1 12.3 - - + +
126B LEU* 3.6 19.5 - - + -
131B PHE* 5.8 0.2 - - + -
136B PRO* 5.2 1.3 - - + -
139B LEU* 3.5 24.7 - - + -
143B GLU 3.0 22.1 + - - +
144B LYS 3.1 7.8 + - - +
146B ARG* 1.4 68.9 - - - +
148B ALA* 1.3 68.4 + - - +
150B ALA* 3.3 6.0 + - - +
151B SER* 2.9 22.7 + - - -
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Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B PRO* 3.6 37.7 - - + -
88B GLU 4.5 2.0 - - - +
91B PHE* 4.1 15.2 - - + -
144B LYS 2.9 15.2 + - - +
145B ARG* 3.3 11.6 + - - +
147B VAL* 1.3 72.3 - - - +
149B ILE* 1.3 62.9 - - + +
151B SER* 2.6 25.3 + - - -
152B VAL* 3.4 10.8 + - - +
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Residues in contact with ILE 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B PRO* 6.4 0.2 - - + -
124B VAL* 3.7 6.5 - - + -
145B ARG* 3.1 19.3 + - + +
146B ARG* 3.9 5.4 - - - +
148B ALA* 1.3 77.2 - - + +
150B ALA* 1.3 65.4 + - - +
152B VAL* 3.0 21.5 + - + +
153B ILE* 3.2 23.5 + - + +
160B LEU* 5.4 8.3 - - + -
162B LEU* 5.5 12.6 - - + -
177B LEU* 3.4 44.2 - - + +
180B ILE* 3.7 38.6 - - + -
181B VAL* 5.8 1.8 - - + -
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Residues in contact with ALA 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B VAL* 3.9 22.4 - - + -
120B ALA* 3.6 22.4 - - + +
121B MET* 4.4 3.6 - - + +
124B VAL* 3.9 7.8 - - + +
126B LEU* 5.2 0.9 - - + -
146B ARG 2.9 18.9 + - - +
147B VAL* 3.3 7.4 + - - +
149B ILE* 1.3 75.0 - - - +
151B SER* 1.3 62.9 + - - +
153B ILE* 3.6 12.0 - - - +
154B VAL* 3.2 27.7 + - - +
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Residues in contact with SER 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B PHE* 5.6 0.3 - - - -
99B GLU* 3.5 33.3 + - - -
100B VAL* 3.9 12.2 - - - +
103B ALA* 3.8 13.6 + - - +
147B VAL 2.9 14.0 + - - -
148B ALA* 2.6 22.3 + - - -
150B ALA* 1.3 78.8 - - - +
152B VAL* 1.3 64.1 + - - +
153B ILE 3.6 0.2 - - - -
154B VAL* 3.6 14.6 - - - +
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Residues in contact with VAL 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B GLY* 3.4 12.7 - - - -
82B ILE 3.7 30.7 - - - +
83B ALA* 4.4 18.4 - - + -
148B ALA 4.0 9.4 - - - +
149B ILE* 3.0 18.8 + - + +
151B SER* 1.3 86.2 + - - +
153B ILE* 1.3 57.3 + - + +
155B HIS* 3.0 22.9 + - - -
157B PRO* 3.5 4.0 - - - +
160B LEU* 3.7 23.8 - - + -
162B LEU* 5.3 1.6 - - + -
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Residues in contact with ILE 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B LYS* 5.7 0.2 + - - -
120B ALA* 4.3 15.6 - - + +
123B PHE* 3.4 37.2 - - + -
124B VAL* 4.8 3.4 - - + -
149B ILE* 3.3 23.8 - - + +
150B ALA* 3.6 13.0 - - - +
152B VAL* 1.3 80.7 - - - +
154B VAL* 1.3 68.3 + - - +
155B HIS 3.1 3.1 - - - -
156B GLU* 2.9 20.6 + - - +
157B PRO* 3.8 5.4 - - - -
160B LEU* 3.9 22.9 - - + -
184B TRP* 3.5 34.1 - - + -
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Residues in contact with VAL 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B VAL* 3.2 25.6 - - + +
103B ALA* 3.9 15.9 - - + -
104B VAL* 3.6 28.3 - - + +
116B LEU* 3.6 38.1 - - - +
117B VAL* 3.9 8.7 - - + +
120B ALA* 3.8 10.5 - - + -
150B ALA 3.2 14.1 + - - +
151B SER 3.6 16.8 - - - +
153B ILE* 1.3 77.2 - - - +
155B HIS* 1.3 60.0 + - + +
156B GLU* 3.1 11.1 + - - +
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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