Contacts of the helix formed by residues 154 - 170 (chain D) in PDB entry 1MVW
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 HIS 154 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17D LEU* 5.0 3.9 - - + +
116D TYR* 2.9 38.1 + + - +
118D TYR* 3.9 5.6 + - - -
123D CYS* 4.4 6.5 - - - -
134D VAL* 3.0 33.5 - - + +
135D TYR* 4.9 0.8 - - - -
139D VAL* 3.9 5.1 - - + +
143D TYR* 2.9 41.0 - - + +
152D PRO 3.1 2.2 + - - -
153D PRO* 1.3 75.5 - - - +
155D ILE* 1.3 74.2 + - + +
156D PHE* 2.9 38.8 - + - +
157D SER* 2.6 35.7 + - - -
158D ILE* 3.5 3.8 + - - +
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Residues in contact with ILE 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D TYR* 4.2 12.9 - - + +
123D CYS* 4.3 11.4 - - - -
125D THR* 4.1 11.4 - - - +
135D TYR* 6.1 1.1 - - + -
154D HIS* 1.3 79.7 - - + +
156D PHE* 1.3 83.0 + - + +
157D SER 2.8 1.3 - - - -
158D ILE* 3.2 8.9 + - + +
159D SER* 3.0 22.1 + - - -
188D ASN* 3.3 40.6 - - + +
191D ARG* 5.8 4.3 - - + -
192D VAL* 4.4 23.3 - - + +
672D VAL* 4.5 23.1 - - + -
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Residues in contact with PHE 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D VAL 3.6 10.8 - - - -
135D TYR* 4.3 22.4 - + + -
139D VAL* 4.2 10.5 - - + -
140D VAL* 3.9 20.4 - - + -
143D TYR* 3.7 22.4 - - + +
154D HIS* 2.9 43.6 - + - -
155D ILE* 1.3 90.1 - - + +
157D SER* 1.3 59.6 + - - +
159D SER* 3.5 5.6 + - - -
160D ASP* 2.7 33.6 + - - +
191D ARG* 4.4 13.9 - - + -
195D TYR* 2.9 48.7 - + + -
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Residues in contact with SER 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D TYR* 3.2 23.7 + - - -
143D TYR* 4.0 25.6 - - - -
146D LYS 4.3 3.4 + - - -
147D LYS 4.6 0.5 + - - -
148D ARG* 3.4 22.2 - - - +
151D ALA* 4.9 1.0 + - - +
152D PRO 4.7 0.3 + - - -
154D HIS 2.6 19.8 + - - -
156D PHE* 1.3 81.1 - - - +
158D ILE* 1.3 59.5 - - - -
160D ASP* 3.9 1.3 - - - -
161D ASN* 2.7 35.2 + - - +
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Residues in contact with ILE 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D TYR* 3.8 17.9 - - + -
121D LEU 5.0 6.1 - - - +
123D CYS* 3.0 45.1 - - + +
148D ARG* 5.6 2.5 - - - +
154D HIS 3.5 3.5 + - - +
155D ILE* 3.2 9.6 + - + +
156D PHE 3.2 0.2 - - - -
157D SER* 1.3 80.7 - - - +
159D SER* 1.3 59.3 + - - +
160D ASP 3.1 0.2 + - - -
161D ASN* 3.2 6.2 + - - +
162D ALA* 2.9 28.9 + - - +
175D ILE* 4.0 26.0 - - + -
192D VAL* 6.5 0.9 - - + -
670D HIS* 4.5 18.6 + - + +
671D PHE 4.4 9.6 - - - +
672D VAL* 4.2 13.5 - - + -
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Residues in contact with SER 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D ILE* 3.0 17.7 + - - -
156D PHE* 3.5 5.8 + - - -
158D ILE* 1.3 80.9 - - - +
160D ASP* 1.3 62.0 + - - +
162D ALA* 4.0 3.1 - - - -
163D TYR 3.8 2.1 + - - -
175D ILE* 4.8 1.6 - - - -
192D VAL* 4.0 25.6 - - - -
195D TYR* 2.8 35.0 - - - -
196D PHE* 3.1 32.4 - - - -
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Residues in contact with ASP 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D TYR 3.4 18.4 - - - +
144D ARG* 2.3 47.0 + - - -
145D GLY* 3.3 7.1 + - - -
146D LYS 4.6 0.8 + - - +
156D PHE 2.7 17.1 + - - +
157D SER 4.0 1.8 - - - +
159D SER* 1.3 77.7 - - - +
161D ASN* 1.3 70.9 + - - +
162D ALA 3.0 1.3 - - - -
163D TYR* 3.0 7.6 + - - +
164D GLN* 2.8 25.8 + - - +
195D TYR* 2.4 33.3 + - - +
199D ILE* 4.1 1.4 - - - +
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Residues in contact with ASN 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D LYS 3.2 22.6 + - - -
147D LYS* 3.6 17.2 - - - +
148D ARG* 4.0 13.7 + - - +
157D SER* 2.7 30.5 + - - +
158D ILE* 3.7 5.4 - - - +
160D ASP* 1.3 81.2 - - - +
162D ALA* 1.3 52.3 + - - +
164D GLN* 2.7 24.1 + - - +
165D PHE* 2.8 60.7 + - + +
670D HIS* 5.2 3.6 - - + -
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Residues in contact with ALA 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D ILE 2.9 16.3 + - - +
159D SER* 3.8 10.3 - - - +
161D ASN* 1.3 78.1 - - - +
163D TYR* 1.3 51.6 + - - +
165D PHE* 3.0 4.9 - - - +
166D MET* 2.6 36.7 + - - +
173D GLN* 3.6 27.8 - - + +
175D ILE* 4.5 10.1 - - + -
196D PHE* 4.3 10.3 - - + -
459D ILE* 4.6 2.5 - - + -
670D HIS* 4.1 11.4 + - + -
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Residues in contact with TYR 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D ARG* 4.1 27.6 - - - +
159D SER 3.8 7.7 + - - +
160D ASP* 3.0 13.6 + - - +
162D ALA* 1.3 77.8 - - - +
164D GLN* 1.3 71.2 + - - +
166D MET* 2.9 30.9 + - - +
167D LEU* 3.0 29.1 + - + +
196D PHE* 4.0 19.3 - + + -
199D ILE* 4.3 15.8 + - + -
200D ALA* 3.1 23.8 - - + +
254D PHE* 4.1 14.6 - + - -
258D GLY* 2.4 38.1 + - - -
259D LYS* 4.4 6.3 + - - -
459D ILE* 4.3 5.1 - - + +
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Residues in contact with GLN 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D ARG* 4.3 8.1 - - - +
145D GLY* 4.2 17.1 - - - +
146D LYS 4.1 4.2 + - - -
147D LYS* 3.0 32.3 - - - +
160D ASP* 2.8 27.0 + - - +
161D ASN* 2.7 46.7 + - - +
163D TYR* 1.3 71.5 - - - +
165D PHE* 1.3 57.1 + - + +
166D MET 2.7 0.5 + - - -
167D LEU* 2.6 35.5 + - - +
168D THR* 2.8 19.9 + - - +
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Residues in contact with PHE 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D LYS* 6.2 4.3 - - + -
161D ASN* 2.8 41.7 + - + +
162D ALA 3.0 5.8 - - - +
164D GLN* 1.3 78.2 - - + +
166D MET* 1.3 66.2 + - - +
168D THR* 3.7 8.1 - - + -
169D ASP* 2.9 52.0 + - - +
170D ARG 3.9 0.2 + - - -
173D GLN* 3.6 17.1 + - - +
668D HIS* 4.5 12.8 - + - -
670D HIS* 3.9 24.5 - + - -
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Residues in contact with MET 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D ALA 2.6 17.8 + - - +
163D TYR* 3.0 24.5 - - - +
164D GLN 2.7 1.4 + - - -
165D PHE* 1.3 79.1 - - - +
167D LEU* 1.3 60.5 + - - -
170D ARG* 3.0 24.3 + - - -
171D GLU 3.7 12.4 + - - +
173D GLN* 3.6 12.3 - - - +
254D PHE* 3.0 52.5 - - + -
258D GLY* 6.0 0.2 - - - -
457D TYR* 3.6 42.7 - - + -
458D PHE 3.6 11.9 - - - +
459D ILE* 3.7 12.3 - - + -
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Residues in contact with LEU 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D ARG* 5.5 3.4 - - - +
163D TYR* 3.0 41.9 + - + +
164D GLN* 2.6 13.1 + - - +
166D MET* 1.3 80.3 - - + +
168D THR* 1.3 62.0 + - - +
170D ARG* 4.0 11.8 + - - +
256D ALA 5.0 1.1 - - - +
257D THR 3.7 9.9 - - - +
258D GLY* 3.6 30.7 - - - -
457D TYR* 4.9 18.7 + - + +
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Residues in contact with THR 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D GLN* 2.8 26.0 + - - +
165D PHE* 4.1 7.4 - - + -
167D LEU* 1.3 75.5 - - - +
169D ASP* 1.3 73.6 + - - +
170D ARG* 4.5 4.0 - - - +
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Residues in contact with ASP 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D PHE* 2.9 41.2 + - - +
168D THR* 1.3 96.1 - - - +
170D ARG* 1.3 72.9 + - - +
171D GLU* 3.3 30.4 + - + +
173D GLN* 5.2 0.2 - - - +
668D HIS* 4.7 6.2 + - - -
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Residues in contact with ARG 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D MET 3.0 14.2 + - - -
167D LEU 4.1 11.4 - - - +
168D THR 3.5 3.6 - - - +
169D ASP* 1.3 82.8 - - - +
171D GLU* 1.3 59.5 - - - +
456D GLN* 5.2 8.9 + - - +
457D TYR* 3.9 39.8 + - + +
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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
------------------------------------------------------------
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