Contacts of the helix formed by residues 187 - 206 (chain A) in PDB entry 3HM5
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 SER 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A HIS* 3.8 4.0 - - - -
185A LYS 4.3 0.2 + - - -
186A ARG* 1.3 75.8 - - - +
188A VAL* 1.3 65.1 + - - +
189A GLU* 3.3 13.0 + - - +
190A ASP* 2.8 44.3 + - - -
191A LEU* 3.1 21.8 + - - +
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Residues in contact with VAL 188 (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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171A PHE* 4.0 28.7 - - + +
172A VAL* 5.0 9.9 - - + +
175A HIS* 3.4 39.1 + - + +
187A SER* 1.3 72.1 - - - +
189A GLU* 1.3 63.2 + - + +
191A LEU* 3.2 8.5 + - - +
192A LYS* 3.0 42.2 + - - +
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Residues in contact with GLU 189 (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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187A SER* 3.1 9.3 + - - +
188A VAL* 1.3 84.0 - - + +
190A ASP* 1.3 57.1 + - - +
192A LYS* 3.4 23.2 + - - +
193A GLU* 3.0 48.8 + - + +
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Residues in contact with ASP 190 (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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152A TRP* 3.9 5.2 + - + +
185A LYS 4.6 2.3 - - - +
186A ARG* 3.7 27.3 + - + +
187A SER* 2.8 47.9 + - - +
189A GLU* 1.3 72.6 - - - +
191A LEU* 1.3 63.8 + - - +
193A GLU* 3.5 5.3 + - - +
194A ARG* 3.1 25.6 + - - +
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Residues in contact with LEU 191 (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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152A TRP* 4.0 6.7 - - + -
160A LEU* 3.9 13.9 - - + +
171A PHE* 4.2 10.0 - - + -
174A ILE* 4.1 17.5 - - + -
175A HIS* 3.9 39.9 - - + +
178A TYR* 3.5 35.0 - - + +
186A ARG* 3.4 26.9 - - + -
187A SER 3.1 10.5 + - - +
188A VAL* 3.2 8.0 + - - +
190A ASP* 1.3 74.3 - - - +
192A LYS* 1.3 65.6 + - - +
194A ARG* 3.4 4.5 + - - +
195A TYR* 3.1 24.1 + - - +
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Residues in contact with LYS 192 (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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171A PHE* 3.6 43.1 - - + -
188A VAL* 3.0 37.1 + - - +
189A GLU* 3.9 20.4 - - - +
191A LEU* 1.3 76.6 - - - +
193A GLU* 1.3 63.7 + - - +
195A TYR* 3.4 0.5 + - - +
196A TYR* 3.0 45.3 + - + +
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Residues in contact with GLU 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A GLU* 3.0 35.3 + - + +
190A ASP* 3.9 6.1 - - - +
192A LYS* 1.3 76.3 - - - +
194A ARG* 1.3 61.0 + - - +
196A TYR* 5.3 2.0 - - - +
197A HIS* 3.0 32.5 + - - +
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Residues in contact with ARG 194 (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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143A TYR* 2.9 27.3 + - - -
147A LEU 2.8 30.1 + - - -
149A ASP* 3.7 24.0 + - - +
152A TRP* 3.4 59.0 - - + +
157A THR* 3.0 16.3 + - - +
160A LEU* 3.8 10.3 - - + -
190A ASP 3.1 9.2 + - - +
191A LEU 3.8 3.8 - - - +
193A GLU* 1.3 78.5 - - - +
195A TYR* 1.3 63.3 + - - +
197A HIS* 3.6 18.9 + - - +
198A ILE* 3.2 45.5 + - + +
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Residues in contact with TYR 195 (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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134A GLN 4.1 1.0 + - - -
135A VAL* 3.2 43.0 - - + +
136A PRO* 3.2 9.1 - - + +
160A LEU* 4.0 5.8 - - + +
161A PHE* 3.5 38.8 - + - -
164A SER* 3.8 22.2 - - - -
169A LEU* 3.7 16.7 - - + +
171A PHE* 4.2 13.0 - + + -
191A LEU 3.1 13.8 + - - +
192A LYS 3.7 3.4 - - - +
194A ARG* 1.3 79.5 - - - +
196A TYR* 1.3 98.7 + + - +
198A ILE* 3.3 4.3 + - - +
199A CYS* 3.1 33.0 + - - -
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Residues in contact with TYR 196 (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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169A LEU* 3.9 20.7 - - + +
171A PHE* 4.2 18.7 - + - -
192A LYS* 3.0 36.6 + - + +
193A GLU* 4.7 1.8 - - - +
195A TYR* 1.3 101.6 - + - +
197A HIS* 1.3 65.8 + - - +
199A CYS* 3.6 14.9 - - + +
200A ALA* 3.0 25.1 + - - +
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Residues in contact with HIS 197 (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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146A TYR 4.8 11.2 - - - -
147A LEU* 5.4 2.2 - - - -
148A HIS 5.3 6.5 - - - -
149A ASP* 5.7 3.8 + - - -
193A GLU 3.0 20.5 + - - +
194A ARG* 3.6 26.7 + - - +
196A TYR* 1.3 74.8 - - - +
198A ILE* 1.3 61.6 + - + +
200A ALA* 3.4 6.1 + - + +
201A LYS* 2.9 41.8 + - + +
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Residues in contact with ILE 198 (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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138A TYR* 4.2 4.0 - - + -
147A LEU* 3.9 30.3 - - + -
157A THR* 3.3 34.5 - - + -
161A PHE* 3.5 30.5 - - + -
194A ARG* 3.2 39.9 + - - +
195A TYR 3.6 6.7 - - - +
197A HIS* 1.3 79.9 - - - +
199A CYS* 1.3 64.8 + - - +
201A LYS* 3.3 1.4 + - - +
202A LEU* 2.9 43.4 + - + +
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Residues in contact with CYS 199 (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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136A PRO* 3.7 27.8 - - + -
161A PHE* 5.2 1.8 - - - -
195A TYR* 3.1 46.5 + - - +
196A TYR* 3.3 21.1 + - + +
198A ILE* 1.3 76.9 - - - +
200A ALA* 1.3 57.1 + - - +
202A LEU* 3.4 5.2 + - - +
203A ALA* 2.9 30.2 + - - +
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Residues in contact with ALA 200 (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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196A TYR 3.0 16.7 + - - +
197A HIS* 3.7 6.1 - - + +
199A CYS* 1.3 73.3 - - - +
201A LYS* 1.3 66.2 + - - +
203A ALA* 3.3 6.6 + - - +
204A ASN* 3.0 33.5 + - - +
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Residues in contact with LYS 201 (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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146A TYR* 3.8 33.7 - - + +
147A LEU* 3.8 15.5 - - + -
197A HIS* 2.9 29.7 + - + +
198A ILE* 3.3 3.8 + - - +
200A ALA* 1.3 75.9 - - - +
202A LEU* 1.3 56.6 + - - +
204A ASN* 3.2 11.9 + - + +
205A VAL* 3.0 44.7 + - + +
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Residues in contact with LEU 202 (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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136A PRO* 3.9 26.9 - - + -
138A TYR* 4.1 19.5 - - + -
142A GLU* 3.8 35.0 - - + +
146A TYR* 5.7 0.4 - - + -
147A LEU* 4.2 13.5 - - + -
198A ILE* 2.9 42.9 + - + +
199A CYS* 3.8 3.4 - - - +
201A LYS* 1.3 68.5 - - - +
203A ALA* 1.3 66.7 + - - +
205A VAL* 4.0 7.6 - - + -
206A ARG* 2.9 52.0 + - - +
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Residues in contact with ALA 203 (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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199A CYS 2.9 18.2 + - - +
200A ALA* 3.5 8.7 - - - +
202A LEU* 1.3 76.3 - - - +
204A ASN* 1.3 66.5 + - - +
206A ARG* 4.1 4.0 - - - +
207A ALA* 3.5 17.2 + - - +
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Residues in contact with ASN 204 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A ALA* 3.0 25.2 + - - +
201A LYS* 3.5 14.2 - - + +
202A LEU 3.2 0.2 - - - -
203A ALA* 1.3 77.2 - - - +
205A VAL* 1.3 67.8 + - + +
207A ALA* 3.2 21.6 + - - +
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Residues in contact with VAL 205 (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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142A GLU* 4.4 7.6 - - - +
146A TYR* 3.8 56.3 - - + +
201A LYS* 3.0 30.2 + - + +
202A LEU* 3.6 17.9 - - + +
204A ASN* 1.3 75.2 - - + +
206A ARG* 1.3 69.7 + - + +
207A ALA 3.2 4.1 + - - -
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Residues in contact with ARG 206 (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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3A UNX 4.3 9.7 - - - -
136A PRO* 4.8 9.3 - - - +
137A VAL 2.7 32.5 + - - +
138A TYR* 3.8 1.8 - - - +
142A GLU* 2.9 39.3 + - - +
202A LEU* 2.9 42.4 + - - +
203A ALA* 4.1 4.5 - - - +
205A VAL* 1.3 79.3 - - + +
207A ALA* 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
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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