Contacts of the helix formed by residues 154 - 166 (chain B) in PDB entry 1R37
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 CYS 154 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B CYS* 4.2 0.9 - - - -
68B HIS* 3.5 9.9 - - + +
69B GLU* 3.3 22.4 - - + +
95B TRP* 3.9 9.2 - - + +
151B PRO 3.3 2.0 + - - -
152B LEU 3.1 1.2 + - - -
153B THR* 1.3 83.5 + - - +
155B SER* 1.3 61.9 + - - +
156B GLY 3.2 0.9 - - - -
157B ILE* 3.8 3.8 - - - -
158B THR* 2.7 37.5 + - - -
403B NAD 3.5 15.7 - - - -
500B ZN 2.3 35.0 - - - -
600B ETX 3.4 7.9 - - - -
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Residues in contact with SER 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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69B GLU* 3.0 13.1 + - - -
151B PRO* 2.8 27.9 + - - +
154B CYS* 1.3 78.2 - - - +
156B GLY* 1.3 51.2 + - - +
159B THR* 2.6 39.2 + - - +
182B GLY 4.0 14.1 + - - -
183B LEU* 3.7 21.8 - - - -
186B MET* 3.6 9.7 - - - +
316B PRO* 5.7 0.2 - - - +
342B ARG* 3.5 18.1 + - - +
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Residues in contact with GLY 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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151B PRO 3.2 5.3 + - - -
152B LEU* 3.7 11.9 - - - -
154B CYS 3.2 0.6 - - - -
155B SER* 1.3 80.9 + - - +
157B ILE* 1.3 59.1 + - - +
159B THR* 3.3 3.6 + - - -
160B TYR* 2.9 30.5 + - - +
186B MET* 3.7 16.4 - - - -
190B ILE* 3.7 2.4 - - - +
305B ILE* 3.7 17.9 - - - -
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Residues in contact with ILE 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ASN* 4.5 9.0 - - - +
95B TRP* 4.0 9.2 - - + +
152B LEU 3.0 14.0 + - - +
153B THR 3.7 22.2 - - - +
154B CYS* 3.5 10.3 - - - +
156B GLY* 1.3 72.7 - - - +
158B THR* 1.3 70.1 + - - +
160B TYR* 3.6 3.7 - - - +
161B ARG* 3.1 22.7 + - - +
296B VAL 3.7 0.8 - - - +
297B GLY* 3.6 22.0 - - - +
298B ASN 3.6 12.6 - - - +
301B ASP* 3.6 16.3 - - + +
302B PHE* 3.5 37.0 - - + +
305B ILE* 4.0 10.2 - - + +
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Residues in contact with THR 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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154B CYS 2.7 25.6 + - - -
157B ILE* 1.3 77.6 - - - +
159B THR* 1.3 58.8 + - - +
161B ARG* 3.3 4.7 + - - +
162B ALA* 3.0 24.4 + - - +
183B LEU* 3.8 8.5 - - + -
270B VAL* 3.7 33.7 - - + -
294B SER* 4.6 3.2 + - - +
295B LEU 5.2 0.2 - - - -
296B VAL* 3.2 29.8 - - - +
403B NAD 3.3 29.2 - - + +
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Residues in contact with THR 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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155B SER 2.6 24.5 + - - +
156B GLY 3.3 5.6 + - - -
158B THR* 1.3 75.0 - - + +
160B TYR* 1.3 59.7 + - - +
162B ALA* 3.7 8.7 - - + +
163B VAL* 2.9 35.7 + - - +
183B LEU* 3.5 43.7 - - + +
186B MET* 3.5 6.9 - - - +
187B ALA* 3.8 21.1 - - + -
190B ILE* 3.4 13.6 - - - +
247B LEU* 4.5 6.5 - - + -
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Residues in contact with TYR 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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156B GLY 2.9 18.4 + - - +
157B ILE* 3.6 8.5 - - - +
158B THR 3.2 0.2 - - - -
159B THR* 1.3 76.6 + - - +
161B ARG* 1.3 65.9 + - - +
163B VAL* 3.4 3.3 + - - +
164B ARG* 3.1 35.0 + - + +
190B ILE* 3.7 25.0 - - + +
194B VAL* 5.7 6.1 - - + -
300B SER 5.1 0.9 - - - -
301B ASP* 4.0 35.2 - - - +
304B GLY* 3.6 30.3 - - - -
305B ILE* 3.8 18.8 - - + -
308B LEU* 4.5 11.0 - - + -
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Residues in contact with ARG 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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264A GLN* 3.6 5.3 - - - +
288A GLU* 2.7 41.7 + - - -
108B GLU* 3.0 20.7 + - - -
110B HIS* 3.6 6.6 + - - -
157B ILE 3.1 14.3 + - - +
158B THR 3.6 2.0 - - - +
160B TYR* 1.3 81.8 - - - +
162B ALA* 1.3 56.4 + - - +
164B ARG* 3.2 27.3 + - - +
165B LYS* 3.0 54.5 + - - +
294B SER* 3.7 9.0 - - - +
295B LEU 3.7 2.9 - - - -
296B VAL 3.2 21.1 - - - +
297B GLY* 3.8 2.0 - - - -
298B ASN* 3.4 15.2 - - - +
301B ASP* 2.9 34.8 + - - +
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Residues in contact with ALA 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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158B THR 3.0 16.6 + - - +
159B THR* 3.9 9.0 - - + +
160B TYR 3.3 0.2 - - - -
161B ARG* 1.3 74.5 - - - +
163B VAL* 1.3 58.9 + - - +
165B LYS* 3.4 3.5 + - - +
166B ALA* 3.1 26.9 + - - +
245B ILE* 3.9 16.4 - - + +
268B VAL* 3.9 24.2 - - + +
270B VAL* 3.9 17.5 - - + -
294B SER* 3.9 8.7 + - - +
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Residues in contact with VAL 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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159B THR 2.9 26.4 + - - +
160B TYR 3.8 4.0 - - - +
162B ALA* 1.3 73.9 - - - +
164B ARG* 1.3 65.4 + - - +
166B ALA* 3.4 13.9 + - - +
167B SER 3.9 3.3 + - - -
168B LEU* 4.1 23.1 + - + +
174B LEU* 5.0 0.2 - - + -
187B ALA* 3.9 22.4 - - - +
190B ILE* 4.2 17.5 - - + +
191B ALA* 4.2 17.0 - - + +
194B VAL* 5.0 5.4 - - + -
195B SER* 5.0 6.7 - - - -
245B ILE* 3.7 20.9 - - + -
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Residues in contact with ARG 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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108B GLU* 5.7 0.4 + - - -
160B TYR* 3.1 25.5 + - + +
161B ARG* 3.2 38.7 - - - +
162B ALA 3.2 0.2 - - - -
163B VAL* 1.3 79.9 - - - +
165B LYS* 1.3 72.7 + - - +
167B SER* 3.1 15.9 + - - -
298B ASN* 4.5 4.4 - - - +
300B SER* 6.3 0.2 - - - -
301B ASP* 3.0 29.3 + - - -
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Residues in contact with LYS 165 (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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264A GLN* 5.0 3.2 - - - +
288A GLU* 3.8 11.4 + - - +
290A GLN* 4.6 15.1 - - - +
161B ARG* 3.0 60.7 + - + +
162B ALA* 3.4 5.8 + - - +
164B ARG* 1.3 81.6 - - - +
166B ALA* 1.3 57.2 + - - +
167B SER* 3.0 18.4 + - - -
266B LYS* 3.5 12.0 - - - +
268B VAL* 4.5 4.2 - - + +
292B VAL* 4.5 20.1 - - + +
293B GLY 4.2 8.5 + - - +
294B SER* 3.4 25.1 - - - +
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Residues in contact with ALA 166 (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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162B ALA 3.1 17.5 + - - +
163B VAL* 3.6 11.7 - - - +
164B ARG 3.2 0.8 - - - -
165B LYS* 1.3 75.5 - - - +
167B SER* 1.3 69.9 + - - +
168B LEU* 3.2 18.2 + - + +
172B LYS* 4.6 2.4 + - - +
174B LEU* 4.8 0.2 - - + -
242B ASP 4.7 1.2 - - - +
243B ALA* 3.7 28.2 - - + +
245B ILE* 4.7 7.4 - - + -
266B LYS* 4.0 9.7 - - - +
268B VAL* 4.1 14.1 - - + +
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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