Contacts of the helix formed by residues 151 - 164 (chain B) in PDB entry 4IYM
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 GLY 151 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85B LEU* 4.5 0.4 - - - +
99B ASP* 3.2 9.0 + - - -
100B ILE* 4.2 5.6 - - - -
149B PHE 3.2 0.6 - - - -
150B PRO* 1.3 81.2 - - - +
152B MSE 1.3 66.4 + - - +
153B ILE 3.4 0.2 - - - -
154B PRO* 3.6 3.5 - - - +
155B MSE 3.1 43.4 + - - +
179B VAL* 3.8 15.3 - - - +
183B LEU* 4.0 2.0 - - - +
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Residues in contact with MSE 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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99B ASP* 2.7 30.0 + - - +
102B ARG* 3.5 46.4 - - + +
103B GLY* 3.9 16.9 - - - +
149B PHE* 3.5 37.9 + - + -
151B GLY* 1.3 73.6 - - - +
153B ILE* 1.3 62.1 + - + +
155B MSE 3.1 4.7 + - - +
156B TRP* 2.7 76.7 + - + +
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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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145B THR* 3.6 19.1 - - + -
146B PRO* 3.7 28.3 - - + -
148B ASN* 4.2 4.0 - - - +
149B PHE* 3.2 27.9 + - + +
152B MSE 1.3 92.0 - - + +
154B PRO* 1.4 75.9 - - + +
156B TRP* 3.3 32.4 - - + +
157B MSE 3.3 12.0 + - + +
222B VAL* 3.8 37.0 - - + -
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Residues in contact with PRO 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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145B THR* 3.8 23.3 - - + +
149B PHE 3.3 15.3 - - - +
150B PRO* 3.3 21.5 - - + +
151B GLY 3.6 8.1 - - - +
153B ILE* 1.4 91.6 - - + +
155B MSE 1.3 57.2 + - - +
157B MSE 3.2 2.8 + - - +
158B PHE* 2.9 40.4 + - + +
170B LEU* 3.8 35.5 - - + +
180B PRO* 4.8 4.0 - - + -
183B LEU* 4.6 4.3 - - + -
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Residues in contact with MSE 155 (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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70B PHE* 4.0 10.3 - - - -
74B LEU* 3.7 20.9 - - + -
100B ILE* 3.6 36.3 - - + +
103B GLY* 3.6 30.7 - - - +
106B VAL* 4.0 2.9 - - - +
107B CYS* 4.1 5.2 - - - -
151B GLY* 3.1 33.3 + - - +
152B MSE 3.1 10.0 + - - +
154B PRO* 1.3 72.7 - - - +
156B TRP* 1.3 66.9 + - - +
158B PHE* 3.7 24.9 - - + -
159B ALA* 3.1 27.9 + - - +
183B LEU* 4.1 17.5 - - + -
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Residues in contact with TRP 156 (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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102B ARG* 4.7 2.8 + - - +
106B VAL* 3.6 29.2 - - + +
152B MSE 2.7 65.7 + - + +
153B ILE* 3.3 34.8 - - + +
155B MSE 1.3 70.0 - - - +
157B MSE 1.3 58.3 + - + +
160B PRO* 3.0 25.5 - - - +
222B VAL* 4.3 9.9 - - + -
441B VAL* 5.1 6.3 - - + -
448B PHE* 3.6 56.3 - + - -
461B GLN* 3.7 32.3 - - + +
462B HIS* 3.8 27.2 + + + -
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Residues in contact with MSE 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B GLY* 3.6 25.8 - - - -
144B ILE 3.6 5.4 - - - +
145B THR* 3.7 22.4 - - + -
153B ILE* 3.6 7.4 - - + +
154B PRO* 3.2 4.7 + - - +
155B MSE 3.1 0.6 - - - -
156B TRP* 1.3 76.9 - - + +
158B PHE* 1.3 64.9 + - - +
159B ALA 3.4 0.2 - - - -
160B PRO* 3.5 5.5 - - - +
161B ALA* 3.2 23.4 + - - +
168B PHE* 3.7 17.3 - - + -
220B SER* 3.6 36.8 - - - +
222B VAL* 3.5 45.5 - - + +
243B GLN* 6.1 0.2 - - - -
461B GLN* 3.7 10.8 - - - +
470B TRP* 3.7 7.7 + - + +
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Residues in contact with PHE 158 (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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67B PHE* 4.7 2.2 - + - -
70B PHE* 4.3 17.5 - + - -
107B CYS* 5.0 0.9 - - - -
154B PRO* 2.9 33.9 + - + -
155B MSE 3.7 31.0 - - + -
157B MSE 1.3 76.4 - - - +
159B ALA* 1.3 74.8 + - + +
161B ALA* 4.2 3.1 - - - -
162B ILE* 2.9 42.4 + - + +
168B PHE* 3.3 33.4 - + + -
170B LEU* 5.1 5.2 - - + -
183B LEU* 4.4 11.7 - - + -
187B MSE 4.2 18.8 - - + -
197B LEU* 3.9 30.1 - - + -
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Residues in contact with ALA 159 (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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67B PHE* 3.3 27.0 - - + -
106B VAL* 3.8 12.8 - - + -
107B CYS* 4.1 14.8 - - - +
110B VAL* 3.8 11.7 - - + -
155B MSE 3.1 16.1 + - - +
158B PHE* 1.3 80.3 - - + +
160B PRO* 1.3 66.8 - - + +
163B ALA* 2.9 30.5 + - - +
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Residues in contact with PRO 160 (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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106B VAL* 3.8 10.5 - - + -
110B VAL* 3.7 15.0 - - + -
156B TRP 3.0 28.9 - - - +
157B MSE 3.5 5.4 - - - +
159B ALA* 1.3 91.2 - - + +
161B ALA* 1.3 64.0 + - - +
163B ALA* 3.9 1.7 - - + +
164B CYS* 3.0 30.1 + - - -
462B HIS* 5.1 0.2 - - - -
466B SER* 3.6 35.7 - - - +
467B ILE* 4.1 9.6 - - + -
470B TRP* 3.9 10.5 - - + +
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Residues in contact with ALA 161 (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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157B MSE 3.2 19.2 + - - +
158B PHE 3.9 1.6 - - - +
160B PRO* 1.3 78.4 - - - +
162B ILE* 1.3 60.0 + - - +
164B CYS 3.6 0.9 + - - -
166B ASN* 2.9 37.7 + - + +
168B PHE* 3.7 25.4 - - + -
470B TRP* 3.4 36.9 - - + -
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Residues in contact with ILE 162 (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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55B TRP* 2.8 41.8 + - + +
67B PHE* 3.8 13.2 - - + -
158B PHE* 2.9 40.5 + - + +
161B ALA* 1.3 71.4 - - - +
163B ALA* 1.3 67.6 + - - +
164B CYS 3.1 2.0 - - - -
165B GLY 2.9 5.9 + - - -
166B ASN 3.6 15.0 - - - +
168B PHE* 4.0 13.7 - - + -
187B MSE 4.3 5.6 - - + -
192B LEU* 3.6 22.2 - - + -
196B ILE* 3.9 10.3 - - + +
197B LEU* 3.8 28.9 - - + -
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Residues in contact with ALA 163 (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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63B ARG* 2.8 34.5 + - - +
67B PHE* 3.7 15.2 - - + -
110B VAL* 3.7 25.4 - - + +
113B ILE* 3.3 28.7 - - + +
159B ALA 2.9 19.9 + - - +
160B PRO 3.9 3.1 - - - +
162B ILE* 1.3 76.6 - - - +
164B CYS* 1.3 54.5 + - - +
165B GLY 3.1 0.2 - - - -
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Residues in contact with CYS 164 (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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63B ARG* 3.9 4.3 + - - -
113B ILE* 3.9 10.3 - - - -
117B GLN* 3.3 21.7 + - - -
137B PRO* 3.5 17.0 - - - +
160B PRO 3.0 23.8 + - - +
162B ILE 3.1 0.4 - - - -
163B ALA* 1.3 76.0 - - - +
165B GLY* 1.3 56.7 + - - +
166B ASN* 3.4 17.9 + - - +
467B ILE* 3.9 27.6 - - - -
470B TRP* 3.7 14.6 - - + +
471B THR* 3.6 22.2 - - + -
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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