Contacts of the helix formed by residues 185 - 201 (chain A) in PDB entry 3M93
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 LYS 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A TYR* 4.9 10.1 - - + +
182A ASP* 3.5 22.4 + - - +
183A SER 3.8 0.2 - - - -
184A LEU* 1.3 73.8 - - - +
186A ASP* 1.3 59.6 + - - +
187A ASP* 3.2 3.6 - - + +
188A VAL* 3.1 24.6 + - + -
189A ASN* 2.8 28.1 + - - -
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Residues in contact with ASP 186 (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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183A SER 4.4 2.8 - - - +
184A LEU 3.6 16.4 - - - +
185A LYS* 1.3 69.4 - - - +
187A ASP* 1.3 74.6 + - - +
189A ASN* 4.2 7.5 + - - -
190A LEU* 2.9 23.0 + - - +
227A ARG* 3.2 35.4 + - - +
228A ILE* 3.8 20.0 - - - +
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Residues in contact with ASP 187 (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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185A LYS 3.2 0.8 - - - -
186A ASP* 1.3 86.1 - - - +
188A VAL* 1.3 63.8 + - + +
190A LEU* 3.6 4.6 - - - +
191A ARG* 2.9 31.2 + - - +
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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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158A ASN* 3.4 40.7 - - + +
161A TYR* 3.5 44.9 - - + +
185A LYS* 3.1 23.2 + - + +
187A ASP* 1.3 78.6 - - + +
189A ASN* 1.3 64.9 + - - +
191A ARG* 3.9 1.2 - - - +
192A ILE* 3.1 34.3 + - + +
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Residues in contact with ASN 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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126A TRP* 3.0 14.1 + - - +
180A THR* 2.9 31.6 + - - +
182A ASP 3.4 18.7 + - - -
183A SER 3.7 9.5 + - - -
185A LYS* 2.8 25.5 + - - +
186A ASP* 4.4 1.6 - - - +
188A VAL* 1.3 72.2 - - - +
190A LEU* 1.3 66.2 + - - +
192A ILE* 3.2 4.2 + - - +
193A GLY 3.0 18.2 + - - -
210A TYR* 3.3 35.5 + - + -
228A ILE* 3.5 18.9 - - + +
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Residues in contact with LEU 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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126A TRP* 4.1 6.7 - - - -
186A ASP 2.9 22.6 + - - +
187A ASP* 3.6 5.4 - - - +
189A ASN* 1.3 71.8 - - - +
191A ARG* 1.3 63.0 + - - +
193A GLY* 3.2 1.9 + - - -
194A GLN* 3.0 50.0 + - - +
228A ILE* 4.0 15.7 - - + +
230A ILE* 3.8 26.7 - - + -
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Residues in contact with ARG 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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155A PHE 5.7 0.2 - - - +
156A GLU* 3.3 35.9 + - - +
158A ASN* 3.7 23.1 - - - +
187A ASP 2.9 17.4 + - - +
188A VAL 3.9 0.7 - - - +
190A LEU* 1.3 76.6 - - - +
192A ILE* 1.3 64.8 + - - +
194A GLN* 3.1 40.9 + - - +
195A ILE* 3.1 40.6 + - + +
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Residues in contact with ILE 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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126A TRP* 3.8 14.1 - - + +
155A PHE* 3.9 21.2 - - + -
158A ASN* 4.5 13.2 - - + -
161A TYR* 4.5 7.6 - - + -
162A ILE* 3.8 15.5 - - + -
178A LEU* 3.6 31.0 - - + -
180A THR* 3.8 20.2 - - - +
188A VAL* 3.1 32.9 + - + +
189A ASN* 3.5 9.6 - - - +
191A ARG* 1.3 75.7 - - - +
193A GLY* 1.3 52.6 + - - +
195A ILE* 3.1 5.4 + - - +
196A LEU* 2.7 32.3 + - + +
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Residues in contact with GLY 193 (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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126A TRP* 3.6 29.8 - - - +
189A ASN 3.0 10.3 + - - -
190A LEU 3.6 2.7 - - - -
192A ILE* 1.3 76.2 - - - +
194A GLN* 1.3 56.3 + - - +
196A LEU* 3.6 7.4 - - - +
197A LYS* 2.9 31.0 + - - +
208A ILE* 3.6 5.2 - - - +
230A ILE* 3.8 9.1 - - - +
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Residues in contact with GLN 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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190A LEU* 3.0 48.7 + - + +
191A ARG* 3.1 43.0 + - - +
192A ILE 3.3 0.2 - - - -
193A GLY* 1.3 76.9 - - - +
195A ILE* 1.3 55.9 + - - +
197A LYS* 3.5 8.4 + - - +
198A ALA* 3.0 26.5 + - - +
230A ILE* 3.9 9.4 - - + +
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Residues in contact with ILE 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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154A GLN* 3.8 24.2 - - + +
155A PHE* 3.5 35.2 - - + +
156A GLU* 3.8 27.6 - - + +
191A ARG* 3.1 34.9 + - + +
192A ILE 3.1 7.7 + - - +
194A GLN* 1.3 73.5 - - - +
196A LEU* 1.3 55.1 + - - +
198A ALA* 3.1 6.7 + - + +
199A LYS* 2.6 53.6 + - + +
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Residues in contact with LEU 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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126A TRP* 3.8 29.8 - - + +
128A VAL* 4.2 21.3 - - + -
146A LEU* 4.2 22.7 - - + -
155A PHE* 4.3 5.4 - - + -
178A LEU* 4.4 20.0 - - + +
192A ILE* 2.7 17.1 + - + +
193A GLY* 3.6 10.3 - - - +
195A ILE* 1.3 71.9 - - - +
197A LYS* 1.3 58.0 + - - +
199A LYS* 4.6 3.4 - - + -
200A LEU* 2.9 55.0 + - + +
202A ILE* 4.8 2.2 - - + -
208A ILE* 4.4 10.3 - - + -
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Residues in contact with LYS 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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193A GLY 2.9 17.7 + - - +
194A GLN* 3.5 7.2 - - - +
196A LEU* 1.3 72.4 - - - +
198A ALA* 1.3 59.1 + - - +
201A GLU* 2.8 24.8 + - - -
202A ILE* 2.8 53.6 + - + +
203A PRO* 3.0 19.4 + - - -
204A ASP* 3.0 31.1 + - - +
206A GLU 4.7 3.8 + - - -
208A ILE* 4.4 11.0 - - + +
230A ILE* 3.7 26.7 + - + +
231A PRO* 4.3 6.3 - - - +
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Residues in contact with ALA 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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194A GLN 3.0 15.1 + - - +
195A ILE* 3.1 10.5 + - + +
197A LYS* 1.3 73.1 - - - +
199A LYS* 1.3 71.2 + - + +
201A GLU* 2.9 21.4 + - - +
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Residues in contact with LYS 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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141A HIS* 4.8 1.4 - - - -
145A GLU* 4.1 24.8 - - + +
149A ALA* 3.9 24.2 - - + +
154A GLN* 3.0 43.2 + - - +
155A PHE* 5.6 0.4 - - + -
195A ILE* 2.6 36.2 + - + +
196A LEU* 4.0 5.6 - - + +
198A ALA* 1.3 77.9 - - + +
200A LEU* 1.3 71.7 + - + +
201A GLU* 3.4 6.9 + - - +
5C ASP* 5.6 1.6 - - - +
6C ARG* 5.3 18.1 - - + +
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Residues in contact with LEU 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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128A VAL* 4.8 3.1 - - + -
141A HIS* 4.5 6.2 - - - -
142A TYR* 3.1 74.3 - - + +
145A GLU* 3.7 13.9 - - + -
146A LEU* 3.7 20.0 - - + +
176A VAL* 4.6 11.2 - - + -
196A LEU* 2.9 40.0 + - + +
199A LYS* 1.3 79.2 - - + +
201A GLU* 1.3 70.7 + - - +
202A ILE* 3.2 18.4 - - + -
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Residues in contact with GLU 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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141A HIS* 4.4 17.6 + - + -
142A TYR* 4.5 2.1 + - - -
197A LYS 2.8 12.2 + - - -
198A ALA* 2.9 16.9 + - - +
199A LYS 4.1 6.0 - - - +
200A LEU* 1.3 80.1 - - - +
202A ILE* 1.3 61.8 + - - +
203A PRO* 3.4 11.1 - - - +
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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