Contacts of the helix formed by residues 183 - 196 (chain A) in PDB entry 4X61
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 GLU 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A TYR* 3.3 22.9 + - - +
180A SER* 2.8 12.5 + - - +
182A GLU* 1.3 76.8 - - - +
184A LYS* 1.3 64.4 + - - +
185A THR* 3.0 5.8 + - - -
186A TRP* 3.0 19.6 + - - +
187A MET* 3.6 5.0 + - - +
216A HIS* 2.7 35.2 + - + +
217A VAL* 3.8 16.8 - - + -
220A ARG* 3.2 37.8 + - + +
544A VAL* 4.2 3.1 - - - +
545A ASN* 3.1 25.2 + - - +
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Residues in contact with LYS 184 (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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129A GLU* 6.2 0.2 - - - +
159A ALA* 4.2 15.9 - - + -
161A GLU* 6.5 0.9 - - - -
162A ASP* 2.8 37.8 + - - +
178A GLU* 4.0 8.7 + - - -
180A SER 3.3 5.1 + - - +
181A GLY* 2.8 30.1 + - - +
182A GLU 3.4 1.5 - - - -
183A GLU* 1.3 77.5 - - - +
185A THR* 1.3 64.7 + - - +
187A MET* 3.2 10.8 + - - +
188A TRP* 3.2 48.0 + - + +
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Residues in contact with THR 185 (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 VAL* 3.3 19.6 - - - +
156A PRO* 2.4 31.5 + - - +
157A LEU 3.0 27.4 - - - +
159A ALA* 4.7 9.9 - - - -
182A GLU 5.0 1.3 - - - +
183A GLU 3.0 3.1 + - - +
184A LYS* 1.3 83.3 - - - +
186A TRP* 1.3 65.2 + - - +
188A TRP* 3.3 29.7 - - - +
189A TRP 3.4 4.2 + - - -
217A VAL* 4.5 8.7 - - + -
221A TRP* 3.9 17.4 - - + +
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Residues in contact with TRP 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 GLU* 3.0 11.4 + - - +
185A THR* 1.3 78.2 - - + +
187A MET* 1.3 77.6 + - + +
189A TRP* 3.1 6.7 + + - +
190A HIS* 2.8 64.4 + + + -
193A ARG* 4.3 1.6 - - - -
217A VAL* 5.8 0.7 - - + -
220A ARG* 3.2 81.8 + - + +
221A TRP* 3.5 33.7 - + + +
224A GLU* 2.9 29.6 + - - -
476A SER* 6.1 0.2 - - - -
546A THR* 5.5 0.2 - - - -
547A VAL* 3.6 22.4 - - + -
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Residues in contact with MET 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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183A GLU 3.6 3.4 + - - +
184A LYS* 3.2 16.4 + - - +
186A TRP* 1.3 101.6 - - + +
188A TRP* 1.3 62.4 + - + +
190A HIS* 4.1 9.4 - - - -
191A ASN* 2.9 61.3 + - - +
220A ARG* 4.1 11.0 - - - +
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Residues in contact with TRP 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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126A LEU* 3.5 29.2 - - + +
127A ASN* 3.4 33.9 - - - -
128A GLN* 3.3 26.5 - - - +
129A GLU* 3.5 37.1 + - + +
131A ASN* 5.0 4.3 + - - +
155A VAL* 4.9 1.3 - - + -
156A PRO* 4.8 8.5 - - + -
159A ALA* 4.1 20.2 - - + -
160A PRO* 4.7 7.0 - - + -
184A LYS* 3.2 48.4 + - + +
185A THR* 3.3 20.9 - - - +
187A MET* 1.3 78.5 - - + +
189A TRP* 1.3 60.6 + - - +
191A ASN* 4.0 5.7 - - - +
192A PHE* 3.3 22.3 + - - +
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Residues in contact with TRP 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 LEU* 3.7 21.5 - - + +
153A MET* 3.8 30.1 - - + -
155A VAL* 4.7 1.8 - - + -
185A THR 3.4 1.5 + - - +
186A TRP* 3.1 12.5 + - - +
188A TRP* 1.3 78.7 - - - +
190A HIS* 1.3 64.8 + - - +
192A PHE* 3.1 5.2 + + - +
193A ARG* 2.9 63.0 + - + +
202A ILE* 3.6 30.5 - - + -
203A ALA 3.9 4.0 - - - -
204A VAL* 3.5 28.6 - - + +
221A TRP* 3.7 32.8 - + + -
224A GLU* 2.8 26.7 + - - -
225A PRO* 3.6 20.0 - - + -
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Residues in contact with HIS 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A TRP* 2.8 48.7 + + + +
187A MET* 3.9 11.4 - - - +
189A TRP* 1.3 75.4 - - - +
191A ASN* 1.3 69.5 - - - +
193A ARG* 2.4 38.9 + - - +
194A THR* 2.7 47.4 + - - +
198A TYR* 4.0 9.4 - - - -
547A VAL* 3.5 26.7 - - + +
591A THR* 5.0 6.2 + - - -
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Residues in contact with ASN 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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129A GLU* 5.0 17.1 + - - +
187A MET* 2.9 45.5 + - - +
188A TRP* 4.0 6.0 - - - +
190A HIS* 1.3 81.9 - - - +
192A PHE* 1.3 58.0 + - - +
194A THR* 3.3 6.2 + - - -
195A LEU* 3.0 39.9 + - + +
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Residues in contact with PHE 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 LEU* 3.8 17.0 - - + -
131A ASN* 4.0 13.5 - - + -
134A LEU* 3.6 17.0 - - + -
135A ALA* 3.4 34.8 - - + -
138A LEU* 3.5 29.2 - - + -
153A MET* 3.5 39.3 - - + -
188A TRP 3.3 16.2 + - - +
189A TRP* 3.1 9.3 + + - +
191A ASN* 1.3 80.7 - - - +
193A ARG* 1.3 64.5 + - - +
195A LEU* 3.4 9.9 + - - +
196A CYS* 3.1 35.5 + - - -
202A ILE* 4.0 7.2 - - + -
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Residues in contact with ARG 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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186A TRP* 4.3 2.2 - - - -
189A TRP* 2.9 53.0 + - + +
190A HIS* 2.4 52.5 + - - +
192A PHE* 1.3 78.1 - - - +
194A THR* 1.3 63.9 + - - +
196A CYS* 3.3 7.5 + - - +
197A ASP 3.1 4.3 + - - -
198A TYR* 3.0 58.6 + - - +
202A ILE* 5.4 4.5 - - + -
224A GLU* 2.5 41.0 + - - -
225A PRO* 5.5 0.2 - - - +
478A SER* 2.6 28.5 + - - -
547A VAL* 5.3 1.2 - - - +
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Residues in contact with THR 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 HIS* 2.7 44.2 + - - +
191A ASN* 3.6 6.7 - - - -
193A ARG* 1.3 75.0 - - - +
195A LEU* 1.3 65.8 + - + +
197A ASP* 3.0 14.2 + - - +
198A TYR* 4.2 20.2 + - + -
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Residues in contact with LEU 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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131A ASN 4.7 1.6 - - - +
132A THR* 3.9 37.0 - - + +
135A ALA* 3.9 25.1 - - + -
139A THR* 4.4 7.1 + - - +
191A ASN* 3.0 28.2 + - + +
192A PHE* 3.6 7.4 - - - +
194A THR* 1.3 77.7 - - + +
196A CYS* 1.3 57.6 + - - +
197A ASP* 3.1 5.6 + - - +
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Residues in contact with CYS 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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135A ALA* 3.9 15.9 - - - -
138A LEU* 4.5 2.7 - - - -
139A THR* 3.4 31.5 + - + +
142A ILE* 5.8 0.4 - - + -
143A HIS* 6.0 1.0 - - - -
192A PHE* 3.1 36.7 + - - +
193A ARG* 3.3 6.0 + - - +
194A THR 3.1 0.4 - - - -
195A LEU* 1.3 75.0 - - - +
197A ASP* 1.3 70.0 + - - +
198A TYR 3.3 1.9 + - - +
199A SER* 3.4 13.8 + - - +
202A ILE* 3.5 32.5 - - + -
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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