Contacts of the helix formed by residues 155 - 171 (chain A) in PDB entry 4MDH
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 THR 155 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A ASN* 4.5 2.5 - - - +
153A CYS* 3.5 18.1 + - - +
154A LEU* 1.3 80.3 - - - +
156A ARG* 1.3 59.4 + - - +
157A LEU* 3.3 3.6 - - - +
158A ASP* 3.4 18.2 - - - +
159A HIS* 3.1 22.3 + - - +
182A ILE* 4.5 6.6 - - + +
186A HIS* 4.0 23.3 - - + +
252A HIS* 4.7 2.0 - - - -
267A SER* 3.8 18.0 + - - -
268A MET* 4.0 1.7 + - - -
269A GLY 4.9 0.7 - - - +
286A SER* 3.1 38.3 + - - -
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Residues in contact with ARG 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 3.7 3.9 - - + +
155A THR* 1.3 76.4 - - - +
157A LEU* 1.3 59.0 + - - +
158A ASP 3.1 1.6 - - - -
159A HIS* 3.6 22.3 + - - -
160A ASN* 3.0 46.2 + - - +
163A LYS* 6.0 1.8 - - - +
248A ALA* 3.7 14.6 - - - +
251A ASP* 3.5 42.5 + - + +
252A HIS* 4.4 16.0 - - + +
255A ASP* 2.7 33.9 + - - +
264A GLU* 5.8 1.0 + - - -
266A VAL* 3.0 30.2 - - - +
267A SER 4.4 10.6 + - - +
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Residues in contact with LEU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 4.7 2.3 - - + +
155A THR* 3.3 1.1 - - - +
156A ARG* 1.3 76.0 - - - +
158A ASP* 1.3 56.6 + - - +
160A ASN* 4.0 1.3 - - - +
161A ARG* 2.8 58.6 + - - +
186A HIS* 5.4 0.2 - - + -
241A SER* 3.3 26.0 - - - +
244A SER* 3.8 28.0 - - - +
245A ALA* 3.5 27.6 - - + +
248A ALA* 3.6 15.0 - - + +
334A SO4 3.5 12.6 - - - +
335A NAD 4.1 14.1 - - + +
58B ASP* 3.8 13.9 - - + +
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Residues in contact with ASP 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A THR* 3.4 22.5 - - - +
157A LEU* 1.3 75.8 - - - +
159A HIS* 1.3 64.7 + - - +
160A ASN 3.2 0.2 - - - -
161A ARG* 2.9 30.9 + - - +
162A ALA* 3.1 11.8 + - - +
182A ILE* 3.5 18.4 - - + +
186A HIS* 2.6 45.8 + - - +
190A GLN* 3.6 32.1 + - - +
226A VAL* 4.1 2.8 - - - +
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Residues in contact with HIS 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A THR 3.1 13.4 + - - +
156A ARG* 3.4 23.0 + - - +
158A ASP* 1.3 81.4 - - - +
160A ASN* 1.3 74.5 + - - +
162A ALA* 3.4 4.0 + - - +
163A LYS* 3.2 40.8 + - + +
180A VAL* 3.8 30.9 + - + +
182A ILE* 3.0 16.4 - - + +
264A GLU* 5.1 6.3 + - - -
265A PHE 4.0 4.9 - - - -
266A VAL* 3.8 24.7 - - + +
267A SER* 3.0 26.1 + - - +
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Residues in contact with ASN 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ARG* 3.0 39.0 + - - +
157A LEU* 4.2 1.8 - - - +
159A HIS* 1.3 78.8 - - - +
161A ARG* 1.3 66.3 + - - +
163A LYS* 3.8 17.3 + - - +
164A ALA* 3.1 22.2 + - - +
247A LYS* 4.2 7.9 - - - +
248A ALA* 4.0 11.5 - - - +
251A ASP* 3.2 22.6 + - - +
58B ASP 3.5 20.9 + - - +
59B CYS* 5.2 0.2 - - - +
60B ALA* 3.9 16.6 - - + +
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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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157A LEU* 2.8 35.2 + - - +
158A ASP* 2.9 26.5 + - - +
160A ASN* 1.3 78.0 - - - +
162A ALA* 1.3 56.3 + - - +
164A ALA* 2.9 25.0 - - - +
165A GLN* 3.1 13.3 + - - +
186A HIS* 4.6 0.2 - - - -
190A GLN* 6.0 0.2 - - - +
226A VAL* 4.0 18.4 + - + -
229A ARG* 3.6 14.5 - - + +
230A GLY* 3.4 26.4 - - - +
233A VAL* 4.3 8.7 - - - +
241A SER* 2.8 28.5 + - - -
244A SER* 5.0 1.6 + - - -
334A SO4 3.1 26.5 + - - -
58B ASP* 2.8 36.6 + - + +
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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 ASP 3.1 7.2 + - - +
159A HIS 3.7 7.6 - - - +
161A ARG* 1.3 73.5 - - - +
163A LYS* 1.3 66.0 + - - +
164A ALA 3.0 1.6 - - - -
165A GLN* 3.0 2.9 + - - +
166A ILE* 3.0 28.8 + - - +
180A VAL* 3.9 17.3 - - + -
182A ILE* 4.1 2.5 - - + -
192A PRO* 4.1 11.4 - - + -
222A PHE* 3.8 20.1 - - + -
226A VAL* 3.6 16.7 - - + +
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Residues in contact with LYS 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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156A ARG* 6.0 1.8 - - - +
159A HIS* 3.2 34.0 + - + +
160A ASN* 3.8 19.2 + - - +
162A ALA* 1.3 77.9 - - - +
164A ALA* 1.3 57.9 + - - +
166A ILE* 3.3 13.6 + - - +
167A ALA* 3.0 28.1 + - - +
174A SER* 3.6 33.3 + - - +
175A ASP* 4.7 8.9 + - - +
177A VAL* 3.3 34.8 + - + +
178A LYS* 5.3 1.1 - - - +
180A VAL* 4.2 16.9 - - + +
264A GLU* 5.1 10.4 + - - -
60B ALA* 4.7 4.8 + - + +
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Residues in contact with ALA 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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160A ASN 3.1 11.7 - - - +
161A ARG* 2.9 16.2 - - - +
162A ALA 3.0 0.2 - - - -
163A LYS* 1.3 80.6 - - - +
165A GLN* 1.3 55.1 + - + +
167A ALA* 3.7 6.7 + - - +
168A LEU* 3.2 36.3 + - + +
174A SER* 4.6 4.9 - - - -
57B GLN* 3.3 33.4 - - + +
58B ASP* 4.6 3.8 - - - +
60B ALA* 4.8 1.1 - - + -
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Residues in contact with GLN 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 3.1 9.1 + - - +
162A ALA 3.0 2.1 + - - +
164A ALA* 1.3 73.5 - - - +
166A ILE* 1.3 65.2 + - - +
168A LEU* 3.7 19.6 + - - +
169A LYS* 3.3 21.7 + - - +
217A TRP* 3.7 10.5 - - + -
222A PHE* 3.4 26.0 - - + -
225A THR* 2.8 37.5 - - + +
226A VAL* 3.4 25.7 - - + +
229A ARG* 3.9 22.9 + - - +
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Residues in contact with ILE 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 3.0 24.2 + - - +
163A LYS 3.3 5.8 + - - +
165A GLN* 1.3 77.6 - - - +
167A ALA* 1.3 56.8 + - - +
169A LYS* 3.0 8.0 - - - +
170A LEU* 2.9 50.4 + - + +
177A VAL* 3.4 39.0 - - + -
180A VAL* 4.1 11.9 - - + -
194A VAL* 4.1 19.5 - - + -
199A VAL* 5.0 0.4 - - + -
208A VAL* 4.2 23.3 - - + -
212A VAL* 5.5 0.9 - - + -
217A TRP* 4.8 4.3 - - + -
218A LEU* 5.3 1.8 - - + -
222A PHE* 4.2 12.1 - - + -
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Residues in contact with ALA 167 (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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163A LYS 3.0 16.7 + - - +
164A ALA* 3.8 7.0 - - - +
165A GLN 3.5 0.2 - - - -
166A ILE* 1.3 72.9 - - - +
168A LEU* 1.3 59.0 + - - +
171A GLY* 2.6 35.7 + - - -
172A VAL* 3.3 19.7 + - + +
173A THR 4.1 7.4 - - - -
174A SER* 4.0 26.0 - - - +
177A VAL* 4.3 1.0 - - + +
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Residues in contact with LEU 168 (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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164A ALA* 3.2 26.5 + - + +
165A GLN* 3.7 21.1 - - - +
166A ILE 3.4 0.2 - - - -
167A ALA* 1.3 78.5 - - - +
169A LYS* 1.3 61.9 + - - +
171A GLY* 3.5 8.4 + - - -
229A ARG* 5.8 0.2 - - - +
57B GLN* 3.5 40.2 - - + +
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Residues in contact with LYS 169 (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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165A GLN 3.3 13.0 - - - +
166A ILE* 3.0 11.7 - - - +
168A LEU* 1.3 82.1 - - - +
170A LEU* 1.3 73.3 + - + +
212A VAL* 4.5 11.0 - - + -
214A ASP* 3.8 13.3 + - - -
217A TRP* 3.4 62.3 - - + +
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Residues in contact with LEU 170 (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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166A ILE* 2.9 39.8 + - + +
169A LYS* 1.3 84.7 - - + +
171A GLY* 1.3 61.3 + - - +
172A VAL* 3.4 16.7 + - + +
199A VAL* 3.6 31.4 - - + -
201A LEU* 5.1 5.6 - - + +
208A VAL* 4.8 0.7 - - + -
211A ALA* 3.9 11.4 - - + +
212A VAL* 3.7 42.8 - - + +
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Residues in contact with GLY 171 (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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167A ALA 2.6 13.8 + - - -
168A LEU* 3.9 7.2 - - - -
169A LYS 3.3 2.8 - - - -
170A LEU* 1.3 79.1 - - - +
172A VAL* 1.3 63.1 + - - +
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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
------------------------------------------------------------
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