Contacts of the helix formed by residues 157 - 167 (chain H) in PDB entry 1R5I
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 GLU 157 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155H ASP* 3.1 36.0 + - + +
156H GLY* 1.3 78.8 - - - +
158H VAL* 1.3 64.2 + - + +
159H ALA 3.4 2.2 - - - -
160H ILE* 3.1 21.2 - - - +
161H ASN* 3.1 28.8 + - - +
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Residues in contact with VAL 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150H LYS 5.1 3.1 - - - +
151H LEU* 5.0 7.9 - - + -
152H ASP* 2.7 36.3 - - + +
153H LEU* 3.8 15.2 - - + +
155H ASP* 4.2 8.5 - - - +
156H GLY 3.7 0.2 - - - -
157H GLU* 1.3 76.7 - - + +
159H ALA* 1.3 65.7 + - - +
161H ASN* 3.2 7.1 + - + +
162H LYS* 2.9 38.0 + - + +
165H GLU* 6.1 0.2 - - - +
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Residues in contact with ALA 159 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153H LEU* 4.0 5.0 - - + +
156H GLY 4.8 0.4 - - - -
157H GLU 3.4 1.0 - - - +
158H VAL* 1.3 79.3 - - - +
160H ILE* 1.3 63.0 + - + +
162H LYS* 3.3 4.5 + - - +
163H VAL* 2.9 30.8 + - - +
184H VAL* 3.8 9.2 - - + +
187H VAL* 3.6 23.3 - - + +
188H TYR* 3.2 42.4 - - + +
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Residues in contact with ILE 160 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156H GLY 2.9 29.6 - - - +
157H GLU* 3.1 28.3 - - - +
159H ALA* 1.3 75.0 - - + +
161H ASN* 1.3 61.3 - - - +
163H VAL* 3.2 10.7 + - + +
164H ARG* 2.9 61.7 + - - +
180H ARG* 4.9 6.7 - - - -
184H VAL* 4.4 21.1 - - + -
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Residues in contact with ASN 161 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157H GLU* 3.1 24.8 + - - +
158H VAL* 3.2 11.2 + - + +
159H ALA 3.2 0.6 - - - -
160H ILE* 1.3 79.8 - - - +
162H LYS* 1.3 65.4 + - - +
164H ARG* 3.1 14.2 + - - +
165H GLU* 2.9 38.8 + - - +
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Residues in contact with LYS 162 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142H MET* 5.5 1.8 - - - -
145H LYS* 6.0 2.0 - - - +
146H LEU* 3.5 33.9 - - + -
149H GLN* 2.9 30.7 + - - +
150H LYS 5.6 1.6 + - - -
151H LEU* 4.9 5.7 - - + +
158H VAL* 2.9 30.7 + - + +
159H ALA* 3.3 6.9 + - - +
161H ASN* 1.3 74.4 - - - +
163H VAL* 1.3 63.3 + - + +
165H GLU* 3.2 29.8 + - - +
166H LEU* 3.0 47.4 + - + +
187H VAL* 5.1 8.7 - - + -
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Residues in contact with VAL 163 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142H MET* 4.9 4.3 - - - -
159H ALA 2.9 17.2 + - - +
160H ILE* 3.2 8.5 + - + +
162H LYS* 1.3 77.8 - - - +
164H ARG* 1.3 57.4 + - + +
167H PHE* 3.0 17.7 + - + +
168H GLY 2.9 19.4 + - - -
173H VAL* 4.2 15.0 - - + -
180H ARG* 4.4 11.2 - - + -
183H LEU* 4.0 31.2 - - + -
184H VAL* 3.7 31.2 - - + +
187H VAL* 4.1 9.6 - - + -
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Residues in contact with ARG 164 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160H ILE* 2.9 37.0 + - - +
161H ASN* 3.5 16.8 - - - +
163H VAL* 1.3 77.2 - - + +
165H GLU* 1.3 61.9 + - - +
168H GLY* 2.9 38.8 + - - +
173H VAL* 5.2 6.8 + - - +
174H LYS* 6.3 0.8 - - - +
180H ARG* 3.7 37.5 - - - +
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Residues in contact with GLU 165 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158H VAL* 6.1 0.5 - - - +
161H ASN* 2.9 34.1 + - - +
162H LYS* 3.2 39.1 + - - +
164H ARG* 1.3 80.4 - - + +
166H LEU* 1.3 70.3 + - + +
168H GLY 4.4 1.7 + - - +
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Residues in contact with LEU 166 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142H MET* 3.8 32.1 - - + -
145H LYS* 3.6 52.0 - - + +
146H LEU* 5.1 2.0 - - + -
162H LYS* 3.0 30.6 + - + +
165H GLU* 1.3 87.0 - - + +
167H PHE* 1.3 85.9 + - + +
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Residues in contact with PHE 167 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138H LEU* 3.3 63.3 - - + -
141H GLU* 4.0 17.3 - - + -
142H MET* 4.2 19.3 - - + -
145H LYS* 6.3 1.3 - - + -
163H VAL* 3.0 13.8 + - - +
166H LEU* 1.3 108.2 - - + +
168H GLY* 1.3 55.1 + - - +
169H SER* 2.5 22.3 + - - -
170H ASP* 2.8 21.9 + - + +
173H VAL* 3.9 22.0 - - + +
183H LEU* 4.4 10.8 - - + -
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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