Contacts of the helix formed by residues 159 - 170 (chain C) in PDB entry 5MR4
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 ASN 159 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158C SER* 1.3 70.3 + - - +
160C HIS* 1.3 58.1 + - - +
161C CYS* 3.1 8.7 + - - +
162C LEU* 3.0 39.9 + - + +
163C ASP* 3.1 33.8 + - - +
226C ASP* 4.6 5.9 + - - +
228C ALA* 4.5 5.5 + - - +
229C CYS* 3.4 38.3 - - - +
232C ARG* 4.6 4.1 - - - +
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Residues in contact with HIS 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C SER* 3.4 29.4 + - - -
159C ASN* 1.3 73.9 + - - +
161C CYS* 1.3 57.8 + - - +
163C ASP* 3.5 15.2 + - + +
164C ALA* 3.0 26.2 + - - +
218C ARG* 4.8 2.9 + - - +
222C CYS* 4.0 12.1 - - + +
223C SER* 3.2 39.0 + - - +
229C CYS* 4.4 4.2 - - - -
356C GLY 4.3 9.2 + - - -
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Residues in contact with CYS 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C ASN* 3.1 6.8 + - - +
160C HIS* 1.3 73.4 - - - +
162C LEU* 1.3 60.3 + - - +
164C ALA* 3.3 4.8 + - - +
165C ALA* 3.0 27.2 + - - +
219C MET* 5.2 2.0 - - - +
222C CYS* 2.1 46.4 - - - -
224C CYS* 3.4 9.9 - - - -
229C CYS* 3.3 28.9 - - - +
232C ARG* 3.7 25.3 - - + +
233C ARG* 3.9 6.1 - - - +
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Residues in contact with LEU 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ARG* 4.1 11.2 - - - +
122A ASP* 4.0 44.0 - - + +
123A GLU* 4.1 8.5 - - + -
159C ASN* 3.0 34.5 + - + +
161C CYS* 1.3 73.8 - - - +
163C ASP* 1.3 67.8 + - - +
165C ALA* 3.3 3.8 + - - +
166C LYS* 3.0 23.7 + - + +
232C ARG* 3.6 35.5 - - - +
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Residues in contact with ASP 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C SER* 3.9 7.7 + - - -
159C ASN 3.1 17.3 + - - +
160C HIS* 3.5 26.0 - - - +
162C LEU* 1.3 77.9 - - - +
164C ALA* 1.3 57.0 + - - +
166C LYS* 3.4 12.3 + - - +
167C ALA* 3.1 28.1 + - - +
218C ARG* 3.5 21.3 + - - +
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Residues in contact with ALA 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C HIS 3.0 17.8 + - - +
161C CYS* 3.5 6.7 - - - +
162C LEU 3.2 0.6 - - - -
163C ASP* 1.3 73.8 - - - +
165C ALA* 1.3 65.8 + - - +
167C ALA* 3.5 3.6 + - - +
168C CYS* 3.1 23.0 + - - +
215C TYR* 5.1 2.1 - - - +
218C ARG* 3.4 50.3 - - + +
219C MET* 3.8 15.2 - - + +
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Residues in contact with ALA 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A GLU* 3.8 29.2 - - + +
124A THR 6.2 0.2 - - - -
161C CYS 3.0 13.8 + - - +
162C LEU* 3.3 7.8 + - - +
164C ALA* 1.3 78.1 - - - +
166C LYS* 1.3 56.0 + - - +
168C CYS* 3.4 6.8 + - - +
169C ASN* 3.0 32.9 + - - +
178C ARG* 4.0 13.4 + - - +
219C MET* 4.5 8.2 - - + +
232C ARG* 4.0 8.5 - - - +
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Residues in contact with LYS 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A GLU* 3.7 24.0 + - - -
123A GLU* 6.4 0.2 - - - +
124A THR* 3.9 36.2 + - - +
162C LEU* 3.0 13.8 + - + +
163C ASP* 3.6 14.1 - - - +
165C ALA* 1.3 73.6 - - - +
167C ALA* 1.3 65.8 + - - +
169C ASN* 3.2 5.8 + - - +
170C LEU* 2.9 45.4 + - + +
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Residues in contact with ALA 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C ASP 3.1 11.3 + - - +
164C ALA 3.5 4.7 + - - +
166C LYS* 1.3 77.9 - - - +
168C CYS* 1.3 62.7 + - - +
170C LEU* 3.5 7.4 + - - +
171C ASN* 3.4 21.3 + - - +
215C TYR* 3.6 21.1 - - + -
218C ARG* 3.5 30.1 - - - +
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Residues in contact with CYS 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C ALA 3.1 16.8 + - - +
165C ALA* 3.6 5.8 - - - +
167C ALA* 1.3 78.0 - - - +
169C ASN* 1.3 58.9 + - - +
171C ASN 2.9 26.5 + - - +
174C CYS* 2.1 61.4 - - - +
175C LYS* 3.2 7.9 + - - -
178C ARG* 3.9 22.2 - - - -
215C TYR* 4.3 4.7 - - + -
219C MET* 3.8 15.5 - - + -
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Residues in contact with ASN 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A GLU* 3.4 12.1 + - - -
124A THR 3.3 27.5 + - - +
125A VAL* 3.9 14.5 - - + +
126A LEU* 4.5 9.9 + - - +
174A VAL* 4.0 8.0 - - + +
175A SER 3.2 23.1 + - - +
176A PHE* 4.7 0.6 - - - +
165C ALA 3.0 13.0 + - - +
166C LYS 4.0 2.0 - - - +
168C CYS* 1.3 75.5 - - - +
170C LEU* 1.3 62.1 + - + +
171C ASN 3.3 2.0 + - - +
175C LYS* 3.7 32.5 - - + +
178C ARG* 3.2 26.7 + - - -
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Residues in contact with LEU 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A GLU* 3.7 40.6 - - + +
124A THR* 4.3 5.8 - - + -
125A VAL* 4.2 4.3 - - - -
126A LEU* 3.8 47.8 - - + +
166C LYS* 2.9 40.2 + - + +
167C ALA* 3.9 6.5 - - - +
168C CYS 3.2 0.4 - - - -
169C ASN* 1.3 77.0 - - + +
171C ASN* 1.3 58.0 + - - +
172C ASP* 4.2 1.4 + - - -
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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