Contacts of the helix formed by residues 182 - 193 (chain C) in PDB entry 1EQB
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 ASP 182 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155C TYR* 2.9 24.9 + - + +
180C VAL* 3.9 1.4 + - - -
181C VAL* 1.3 70.2 - - - +
183C TRP* 1.3 62.3 + - - +
184C ALA* 3.3 10.9 + - - +
185C LYS* 2.7 44.3 + - + +
186C MET* 3.1 24.3 + - - +
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Residues in contact with TRP 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C GLY* 4.2 12.1 - - - -
173C GLY* 4.5 10.3 - - - -
174C PHE* 4.7 4.3 - + - -
181C VAL* 3.1 39.5 + - + -
182C ASP* 1.3 71.8 + - - +
184C ALA* 1.3 63.2 + - - +
186C MET* 3.2 9.9 + - + +
187C ARG* 3.0 23.4 + - - +
197C LEU* 3.7 5.0 - - + +
199C VAL* 3.7 36.3 - - + -
200C ASP 5.5 0.7 - - - -
201C MET* 5.4 1.3 - - + -
204C VAL* 5.1 7.9 - - + -
213C TYR* 3.9 20.4 - + - -
214C PRO* 2.9 39.4 + - + +
215C ASN 3.6 5.4 - - - -
216C PRO* 3.3 37.3 - - + +
219C HIS* 3.9 21.3 - + + +
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Residues in contact with ALA 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C ASP* 3.3 7.0 + - - +
183C TRP* 1.3 79.6 - - - +
185C LYS* 1.3 56.7 + - - +
187C ARG* 3.2 4.8 + - - +
188C GLU* 2.9 32.7 + - - +
219C HIS* 3.6 32.3 - - + +
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Residues in contact with LYS 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C TYR* 3.8 36.3 - - + -
159C GLU* 4.0 19.7 + - - -
182C ASP* 2.7 39.0 + - + +
184C ALA* 1.3 69.6 - - - +
186C MET* 1.3 65.3 + - - +
188C GLU* 3.3 36.0 + - - +
189C ILE* 3.2 32.8 + - + +
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Residues in contact with MET 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C TYR* 3.6 24.7 - - + +
153C ILE* 5.7 2.5 - - + -
155C TYR* 4.1 15.0 - - + -
158C LEU* 4.0 17.9 - - + -
170C ILE* 3.9 27.7 - - + +
172C GLY* 3.8 20.6 - - - +
181C VAL* 3.7 25.1 - - - -
182C ASP 3.1 14.8 + - - +
183C TRP* 3.6 12.6 - - - +
185C LYS* 1.3 74.1 - - - +
187C ARG* 1.3 60.9 + - - +
189C ILE* 3.3 10.5 + - - +
190C ALA* 2.9 27.4 + - - +
197C LEU* 3.9 16.5 - - + +
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Residues in contact with ARG 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C TRP 3.0 11.9 + - - +
184C ALA* 3.5 9.9 - - - +
186C MET* 1.3 76.0 - - - +
188C GLU* 1.3 65.5 + - - +
190C ALA* 3.2 2.1 + - - -
191C ASP* 2.8 52.1 + - - +
197C LEU* 3.5 8.9 - - + +
218C PRO 5.1 1.4 + - - -
219C HIS* 2.6 61.0 + - + +
220C ALA 4.1 9.9 + - - +
221C HIS* 3.5 36.5 + - - +
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Residues in contact with GLU 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C ALA* 2.9 17.7 + - - +
185C LYS* 3.3 42.0 + - + +
186C MET 3.2 0.2 - - - -
187C ARG* 1.3 79.6 - - - +
189C ILE* 1.3 64.4 + - + +
191C ASP* 3.1 8.0 + - - +
192C SER* 3.1 21.2 + - - -
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Residues in contact with ILE 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C TYR* 3.7 28.5 - - + +
158C LEU* 3.8 26.7 - - + +
159C GLU* 3.9 29.8 - - + +
162C ALA* 3.6 29.4 - - + -
170C ILE* 4.0 9.2 - - + -
185C LYS* 3.2 22.6 + - + +
186C MET* 3.5 9.2 - - - +
187C ARG 3.3 0.2 - - - -
188C GLU* 1.3 77.0 - - + +
190C ALA* 1.3 60.7 + - - +
192C SER* 2.6 24.8 + - - +
193C ILE* 3.7 7.1 + - - +
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Residues in contact with ALA 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C ILE* 4.1 15.9 - - + +
186C MET 2.9 17.1 + - - +
187C ARG* 3.6 9.2 - - - +
189C ILE* 1.3 74.7 - - - +
191C ASP* 1.3 64.4 + - - +
193C ILE* 3.0 5.0 + - - +
194C GLY 2.9 4.5 + - - -
195C ALA* 2.9 47.4 + - + +
196C TYR 4.5 0.4 - - - -
197C LEU* 4.2 20.2 - - + +
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Residues in contact with ASP 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C ARG* 2.8 54.2 + - - +
188C GLU* 3.4 7.9 - - - +
190C ALA* 1.3 77.3 - - - +
192C SER* 1.3 62.0 + - - +
193C ILE 3.2 0.9 + - - -
194C GLY* 3.2 12.5 + - - +
195C ALA 4.9 1.3 - - - +
221C HIS* 4.4 6.2 + - - -
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Residues in contact with SER 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C GLU* 5.4 5.4 - - - +
162C ALA* 5.9 0.2 - - - +
188C GLU 3.1 10.1 + - - -
189C ILE* 2.6 27.4 + - - +
191C ASP* 1.3 76.8 - - - +
193C ILE* 1.3 66.9 + - - +
194C GLY 3.5 0.2 - - - -
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Residues in contact with ILE 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C ALA* 3.6 27.4 - - + +
163C LYS* 4.2 15.3 - - + +
166C LYS* 4.3 10.2 - - + +
167C PRO* 3.4 49.7 - - + +
170C ILE* 4.4 2.5 - - + -
189C ILE 3.8 6.1 - - - +
190C ALA 3.4 10.8 - - - +
192C SER* 1.3 87.9 + - - +
194C GLY* 1.3 62.9 + - - +
195C ALA* 3.8 9.9 - - + +
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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