Contacts of the helix formed by residues 187 - 201 (chain C) in PDB entry 5Z7R
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 187 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183C VAL* 3.3 18.6 - - + +
184C GLU* 2.9 40.3 + - + +
186C SER* 1.3 83.1 - - - +
188C LEU* 1.3 59.1 + - - +
189C MET 3.6 0.9 - - - -
190C ASN* 3.4 11.3 + - + +
191C THR* 2.9 37.2 + - + +
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Residues in contact with LEU 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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55C THR* 5.0 1.3 - - - +
103C ALA* 4.0 17.5 - - + +
104C VAL 3.9 4.9 - - - +
105C ASN* 3.4 39.9 - - + -
123C ILE* 3.3 33.9 - - + +
124C ALA* 3.7 6.7 - - - +
125C SER* 3.7 25.4 - - - +
183C VAL* 3.8 4.7 - - + -
184C GLU 3.3 6.9 + - - +
185C PRO 3.7 13.0 + - - +
186C SER 3.5 1.8 - - - -
187C GLU* 1.3 76.6 - - - +
189C MET* 1.3 68.4 + - + +
191C THR* 2.6 21.7 + - - +
192C ALA* 3.0 9.9 + - - +
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Residues in contact with MET 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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16C VAL* 4.1 18.4 - - + -
53C ILE* 3.9 18.8 - - + -
55C THR* 4.2 19.5 - - + -
103C ALA* 4.1 22.9 - - - -
185C PRO 5.1 0.6 + - - -
186C SER 5.4 1.0 - - - -
188C LEU* 1.3 82.7 - - + +
190C ASN* 1.3 64.6 + - - +
192C ALA* 3.6 2.3 - - - +
193C LYS* 2.9 62.7 + - + +
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Residues in contact with ASN 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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186C SER 4.0 16.3 + - - -
187C GLU* 3.4 12.2 + - + +
188C LEU 3.2 0.6 - - - -
189C MET* 1.3 80.4 - - - +
191C THR* 1.3 57.7 + - + +
193C LYS* 3.4 11.2 + - - +
194C GLU* 2.9 29.4 + - - +
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Residues in contact with THR 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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123C ILE* 4.2 11.7 - - - +
181C LYS* 5.3 10.5 - - - +
183C VAL* 3.9 26.0 - - + +
187C GLU* 2.9 29.9 + - + +
188C LEU* 2.6 24.6 + - - -
190C ASN* 1.3 73.4 - - + +
192C ALA* 1.3 59.6 + - - +
194C GLU* 3.3 17.3 + - - +
195C ILE* 2.9 40.5 + - - +
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Residues in contact with ALA 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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53C ILE* 3.8 19.1 - - + -
101C ILE* 3.8 14.0 - - + +
103C ALA* 4.1 22.9 - - + -
123C ILE* 4.7 4.2 - - + +
188C LEU 3.0 11.8 + - - +
189C MET* 3.6 6.5 - - - +
191C THR* 1.3 78.5 + - - +
193C LYS* 1.3 59.6 + - - +
195C ILE* 3.2 10.8 + - - +
196C ALA* 2.8 29.6 + - - +
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Residues in contact with LYS 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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11C GLU* 3.1 35.4 + - + +
14C VAL* 5.5 6.3 - - + -
16C VAL* 4.9 4.6 - - + +
53C ILE* 3.8 21.7 - - + +
189C MET* 2.9 49.9 + - + +
190C ASN* 3.7 10.5 - - - +
192C ALA* 1.3 77.2 - - - +
194C GLU* 1.3 57.4 + - - +
196C ALA* 3.7 1.5 - - + +
197C ASN* 2.8 48.4 + - - +
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Residues in contact with GLU 194 (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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166B GLN* 5.5 6.6 + - - +
181C LYS* 5.8 1.7 + - - -
190C ASN 2.9 16.1 + - - +
191C THR* 3.5 18.9 - - - +
192C ALA 3.3 0.2 - - - -
193C LYS* 1.3 76.3 - - - +
195C ILE* 1.3 62.4 + - + +
197C ASN* 4.0 7.0 - - - +
198C LYS* 3.2 23.3 + - + +
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Residues in contact with ILE 195 (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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160B GLN* 4.0 14.8 - - + +
164B THR* 4.3 14.1 - - + +
166B GLN* 5.8 3.8 - - - +
101C ILE* 3.5 21.5 - - + -
121C ILE* 4.7 9.2 - - + -
123C ILE* 3.4 38.6 - - + -
181C LYS* 6.0 3.4 - - + -
191C THR* 2.9 22.1 + - - +
192C ALA* 3.5 9.0 - - - +
194C GLU* 1.3 75.9 - - + +
196C ALA* 1.3 66.3 + - - +
198C LYS* 3.1 6.9 + - - +
199C ILE* 3.1 34.1 + - + +
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Residues in contact with ALA 196 (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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14C VAL* 4.1 20.2 - - + -
51C ALA* 4.0 7.6 - - + +
53C ILE* 4.0 16.4 - - + -
101C ILE* 3.7 17.5 - - + -
192C ALA 2.8 20.2 + - - +
193C LYS* 3.7 4.3 - - - +
195C ILE* 1.3 73.6 - - - +
197C ASN* 1.3 57.3 + - - +
199C ILE* 3.4 7.2 + - - +
200C VAL* 3.0 32.9 + - - +
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Residues in contact with ASN 197 (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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12C GLY* 6.1 0.5 - - - -
14C VAL* 3.7 18.7 - - - +
193C LYS* 2.8 38.4 + - - +
194C GLU* 4.0 6.9 - - - +
196C ALA* 1.3 71.5 - - - +
198C LYS* 1.3 61.5 + - - +
200C VAL* 3.7 9.8 - - - +
201C SER* 2.9 28.9 + - - -
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Residues in contact with LYS 198 (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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164B THR* 3.3 31.6 + - + +
165B ALA* 6.0 0.6 - - - +
166B GLN* 3.7 35.2 - - + +
194C GLU* 3.2 16.1 + - + +
195C ILE* 3.1 5.9 + - - +
197C ASN* 1.3 74.6 - - - +
199C ILE* 1.3 65.7 - - - +
201C SER* 3.1 26.7 + - - -
202C ASN* 3.1 16.0 + - - +
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Residues in contact with ILE 199 (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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163B PHE* 3.7 46.2 - - + +
164B THR* 3.9 6.1 - - + -
50C LEU 4.3 9.9 - - - +
51C ALA* 4.4 4.0 - - + -
99C PRO* 3.8 30.1 - - + -
101C ILE* 4.4 8.5 - - + -
121C ILE* 4.3 8.3 - - + -
195C ILE* 3.1 29.0 + - + +
196C ALA* 3.5 8.5 - - - +
197C ASN 3.2 0.2 - - - -
198C LYS* 1.3 76.1 - - - +
200C VAL* 1.3 53.4 + - - +
202C ASN* 2.8 34.1 + - - +
207C VAL* 4.1 15.4 - - + +
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Residues in contact with VAL 200 (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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13C LYS* 3.9 38.3 - - + +
14C VAL* 4.6 2.9 - - + -
50C LEU* 3.5 39.2 - - + +
51C ALA* 3.7 17.0 - - + -
196C ALA 3.0 17.6 + - - +
197C ASN* 3.7 13.0 - - - +
199C ILE* 1.3 72.9 - - - +
201C SER* 1.3 61.8 + - - +
202C ASN 3.1 12.6 + - - +
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Residues in contact with SER 201 (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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197C ASN 2.9 18.3 + - - -
198C LYS* 3.1 33.4 + - - -
199C ILE 3.1 1.0 - - - -
200C VAL* 1.3 78.3 - - - +
202C ASN* 1.3 61.0 + - - +
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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