Contacts of the helix formed by residues 154 - 166 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A CYS* 4.1 0.7 - - - -
68A HIS* 3.5 9.4 - - + -
69A GLU* 3.4 22.2 - - + +
95A TRP* 4.0 8.1 - - + +
151A PRO 3.4 1.6 + - - -
152A LEU 3.1 1.0 - - - -
153A THR* 1.3 81.7 + - - +
155A SER* 1.3 62.1 - - - +
156A GLY 3.1 0.4 - - - -
157A ILE* 3.8 4.3 - - - -
158A THR* 2.8 37.8 + - - -
403A NAD 3.4 15.9 - - - -
500A ZN 2.3 35.0 - - - -
600A ETX 3.3 8.1 - - - -
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Residues in contact with SER 155 (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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69A GLU* 3.0 11.4 + - - -
151A PRO* 2.6 28.6 + - - +
154A CYS* 1.3 79.2 - - - +
156A GLY* 1.3 52.3 + - - +
159A THR* 2.6 39.3 + - - +
182A GLY 4.1 12.5 + - - -
183A LEU* 3.7 22.2 - - - -
186A MET* 3.6 10.4 - - - +
316A PRO* 5.7 0.3 - - - +
342A ARG* 3.6 18.0 + - - +
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Residues in contact with GLY 156 (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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151A PRO 3.2 4.9 + - - -
152A LEU* 3.7 11.9 - - - -
154A CYS 3.1 0.4 - - - -
155A SER* 1.3 80.5 + - - +
157A ILE* 1.3 59.3 + - - +
159A THR* 3.2 3.6 + - - -
160A TYR* 2.8 31.0 + - - +
186A MET* 3.7 15.7 - - - -
190A ILE* 3.7 2.1 - - - +
305A ILE* 3.7 17.7 - - - -
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Residues in contact with ILE 157 (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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93A ASN* 4.5 8.5 - - - +
95A TRP* 4.1 10.3 - - + +
152A LEU 3.0 13.6 + - - +
153A THR 3.7 21.8 - - - +
154A CYS* 3.4 11.4 - - - +
156A GLY* 1.3 73.6 - - - +
158A THR* 1.3 68.0 + - - +
160A TYR* 3.7 3.1 - - - +
161A ARG* 3.1 23.7 + - - +
296A VAL 3.5 0.4 - - - +
297A GLY* 3.6 31.2 - - - +
298A ASN 3.6 3.4 - - - +
301A ASP* 3.7 16.1 - - + +
302A PHE* 3.5 37.0 - - + +
305A ILE* 4.0 11.6 - - + +
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Residues in contact with THR 158 (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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154A CYS 2.8 25.3 + - - -
155A SER 4.3 2.2 - - - -
157A ILE* 1.3 79.3 - - - +
159A THR* 1.3 58.4 + - - +
161A ARG* 3.4 3.8 + - - +
162A ALA* 3.0 24.9 + - - +
183A LEU* 3.9 6.1 - - + -
270A VAL* 3.7 32.3 - - + -
294A SER* 4.5 3.5 + - - +
296A VAL* 3.2 30.8 - - - +
403A NAD 3.3 31.5 - - + +
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Residues in contact with THR 159 (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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155A SER 2.6 24.2 + - - +
156A GLY 3.2 5.4 + - - -
158A THR* 1.3 75.2 - - + +
160A TYR* 1.3 59.5 + - - +
162A ALA* 3.7 7.1 - - + +
163A VAL* 2.9 36.4 + - - +
183A LEU* 3.4 44.0 - - + +
186A MET* 3.5 7.1 - - - +
187A ALA* 3.8 22.2 - - + -
190A ILE* 3.5 12.2 - - - +
245A ILE* 5.6 0.2 - - + -
247A LEU* 4.4 6.5 - - + -
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Residues in contact with TYR 160 (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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156A GLY 2.8 18.0 + - - +
157A ILE* 3.7 5.8 - - - +
158A THR 3.2 0.2 - - - -
159A THR* 1.3 78.8 + - - +
161A ARG* 1.3 64.8 + - - +
163A VAL* 3.3 2.8 + - - +
164A ARG* 3.1 33.3 + - + +
190A ILE* 3.8 24.5 - - + +
194A VAL* 5.7 5.8 - - + -
300A SER 5.1 0.4 - - - -
301A ASP* 4.0 33.2 - - - -
304A GLY* 3.5 29.9 - - - -
305A ILE* 3.8 26.7 - - + -
308A LEU* 4.5 10.8 - - + -
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Residues in contact with ARG 161 (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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108A GLU* 2.9 24.2 + - - -
110A HIS* 3.6 5.6 + - - -
157A ILE 3.1 14.9 + - - +
158A THR 3.7 1.3 - - - +
160A TYR* 1.3 80.1 - - - +
162A ALA* 1.3 57.3 + - - +
164A ARG* 3.0 28.9 + - - +
165A LYS* 2.9 53.2 + - - +
294A SER* 3.7 8.7 - - - +
295A LEU 3.8 3.4 - - - -
296A VAL 3.2 21.3 - - - +
297A GLY* 3.8 1.8 - - - -
298A ASN* 3.3 14.6 - - - +
301A ASP* 2.9 36.1 + - - +
264B GLN* 3.7 4.9 - - - +
288B GLU* 2.7 41.9 + - - -
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Residues in contact with ALA 162 (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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158A THR 3.0 18.1 + - - +
159A THR* 3.8 9.2 - - - +
160A TYR 3.3 0.2 - - - -
161A ARG* 1.3 77.6 - - - +
163A VAL* 1.3 60.6 + - - +
165A LYS* 3.3 3.6 + - - +
166A ALA* 3.1 22.3 + - - +
245A ILE* 3.9 15.2 - - + +
268A VAL* 3.9 15.6 - - + +
270A VAL* 3.9 26.7 - - + -
294A SER* 3.9 9.3 + - - +
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Residues in contact with VAL 163 (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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159A THR 2.9 27.3 + - - +
160A TYR 3.8 3.8 - - - +
161A ARG 3.3 0.2 - - - -
162A ALA* 1.3 76.3 - - - +
164A ARG* 1.3 61.9 + - - +
166A ALA* 3.5 15.0 + - - +
167A SER 3.9 2.4 + - - -
168A LEU* 4.1 24.3 + - + +
187A ALA* 3.9 23.1 - - - +
190A ILE* 4.3 17.5 - - + +
191A ALA* 4.2 17.5 - - + +
194A VAL* 5.0 5.6 - - + -
195A SER* 4.9 6.1 - - - -
245A ILE* 3.7 21.3 - - + -
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Residues in contact with ARG 164 (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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108A GLU* 5.7 0.4 + - - -
160A TYR* 3.1 24.6 + - + +
161A ARG* 3.0 41.8 - - - +
163A VAL* 1.3 77.1 - - - +
165A LYS* 1.3 73.2 + - - +
167A SER* 3.1 16.5 + - - -
298A ASN* 4.5 4.0 - - - +
300A SER* 6.3 0.2 - - - -
301A ASP* 2.9 28.3 + - - -
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Residues in contact with LYS 165 (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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161A ARG* 2.9 60.6 + - + +
162A ALA* 3.3 5.4 + - - +
164A ARG* 1.3 82.1 - - - +
166A ALA* 1.3 57.2 + - - +
167A SER* 3.0 17.9 + - - -
266A LYS* 3.5 12.8 - - - +
268A VAL* 4.5 4.3 - - + +
292A VAL* 4.6 19.1 - - + +
293A GLY 4.2 8.3 - - - +
294A SER* 3.5 24.2 - - - +
264B GLN* 5.1 3.4 - - - +
288B GLU* 3.8 11.7 + - - +
290B GLN* 4.8 13.8 - - - +
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Residues in contact with ALA 166 (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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162A ALA 3.1 13.9 + - - +
163A VAL* 3.6 14.8 - - - +
164A ARG 3.1 0.8 - - - -
165A LYS* 1.3 74.4 - - - +
167A SER* 1.3 70.4 + - - +
168A LEU* 3.2 13.8 + - + +
172A LYS* 4.7 2.1 + - - +
174A LEU* 4.9 0.2 - - + -
242A ASP 4.8 1.6 - - - +
243A ALA* 3.7 32.6 - - + +
245A ILE* 4.7 7.2 - - + -
266A LYS* 4.0 9.7 - - - +
268A VAL* 4.1 13.7 - - + -
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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