Contacts of the helix formed by residues 190 - 201 (chain C) in PDB entry 1QQW
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 PRO 190 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186C TRP 4.0 4.4 - - - +
187C SER 4.5 5.6 - - - +
188C LEU* 3.3 10.8 - - - +
189C ARG* 1.3 86.7 - - - +
191C GLU* 1.3 63.1 + - - +
192C SER 3.1 0.9 - - - -
193C LEU* 3.2 35.0 - - + +
435C ALA 5.2 2.7 - - - +
439C ASN* 3.2 26.5 - - + +
440C VAL* 6.3 1.3 - - + -
481C ASN* 3.9 23.6 - - + +
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Residues in contact with GLU 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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153C PHE 4.6 0.9 - - - +
154C PHE 3.3 16.2 - - - +
155C ILE* 3.4 23.6 - - + +
156C ARG* 3.8 27.7 + - - +
160C LEU* 4.4 3.5 - - - +
189C ARG* 2.7 59.4 + - - +
190C PRO* 1.3 77.8 - - - +
192C SER* 1.3 65.7 + - - +
193C LEU* 3.2 1.0 + - - +
194C HIS* 3.9 9.4 + - - +
300C THR* 4.1 17.3 - - + +
435C ALA* 4.4 6.0 - - - +
439C ASN* 3.4 31.3 - - - +
443C VAL* 5.9 0.2 - - - +
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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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154C PHE* 2.9 30.0 + - - -
155C ILE* 5.7 0.2 - - - -
185C PHE* 5.5 1.6 - - - -
186C TRP* 3.3 41.1 + - - -
189C ARG* 2.8 21.4 + - - -
190C PRO* 4.8 0.2 - - - +
191C GLU* 1.3 78.1 - - - +
193C LEU* 1.3 67.5 + - - +
194C HIS 3.3 0.2 - - - -
195C GLN* 3.1 7.3 + - - +
196C VAL* 2.9 23.9 + - - +
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Residues in contact with LEU 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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186C TRP 6.1 0.4 - - - +
190C PRO* 3.2 27.9 + - + +
191C GLU 3.1 0.8 - - - -
192C SER* 1.3 80.0 + - - +
194C HIS* 1.3 58.7 + - - +
196C VAL* 3.0 9.3 + - + +
197C SER* 2.5 35.6 + - - +
439C ASN 3.9 12.6 - - - +
440C VAL* 4.8 4.3 - - + -
443C VAL* 4.4 5.8 - - + -
481C ASN* 3.5 28.7 - - + +
482C PHE* 3.8 38.6 - - + -
485C VAL* 3.4 26.5 - - + -
489C TYR* 5.4 0.4 - - + -
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Residues in contact with HIS 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C ILE* 3.6 18.8 - - + +
153C PHE 5.4 0.9 - - - +
191C GLU 3.9 9.2 + - - +
192C SER 3.1 1.0 + - - -
193C LEU* 1.3 78.3 - - - +
195C GLN* 1.3 63.6 - - - +
197C SER* 3.3 14.8 + - - -
198C PHE* 3.3 11.0 + + + +
300C THR* 3.3 24.6 + - - +
302C VAL* 4.4 16.0 - - + +
442C GLN* 3.2 53.4 + - + +
443C VAL* 3.6 23.6 - - + +
446C PHE* 4.6 17.7 - + + +
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Residues in contact with GLN 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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129C PRO* 4.4 8.1 - - - +
150C THR* 2.7 46.7 + - - +
152C ILE* 3.1 20.8 - - + +
153C PHE* 3.5 22.9 + - - +
154C PHE* 3.3 44.8 - - + +
192C SER 3.1 6.7 + - - +
194C HIS* 1.3 76.0 - - - +
196C VAL* 1.3 54.2 + - - +
198C PHE* 3.0 10.1 + - - +
199C LEU* 2.8 38.0 + - - +
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Residues in contact with VAL 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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154C PHE* 3.9 7.6 - - + -
183C TRP* 4.6 7.4 - - + -
186C TRP* 3.7 36.8 - - + +
192C SER* 2.9 27.5 + - - +
193C LEU* 3.3 12.1 - - + +
195C GLN* 1.3 75.6 - - - +
197C SER* 1.3 65.2 + - - +
199C LEU* 3.0 5.2 + - - +
200C PHE* 2.9 46.6 + - + -
463C ILE* 4.7 2.2 - - + -
482C PHE* 4.5 22.9 - - + -
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Residues in contact with SER 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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193C LEU* 2.5 27.2 + - - +
194C HIS 3.3 6.7 + - - -
196C VAL* 1.3 75.5 - - - +
198C PHE* 1.3 61.8 + - - +
201C SER* 3.3 10.2 + - - -
443C VAL* 3.6 14.6 - - - +
446C PHE* 3.9 25.7 - - - -
447C TYR* 6.5 0.2 - - - -
459C LEU* 3.2 25.0 - - - +
489C TYR* 3.5 27.3 + - - -
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Residues in contact with PHE 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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149C ASN* 4.2 16.6 - - - -
150C THR* 4.1 24.0 - - - -
151C PRO* 4.2 15.7 - - + -
152C ILE* 4.7 6.3 - - + -
194C HIS* 3.3 9.0 + + + +
195C GLN* 3.0 17.6 + - - +
197C SER* 1.3 78.0 - - - +
199C LEU* 1.3 68.7 + - - +
201C SER* 3.1 19.1 + - - -
203C ARG* 3.5 61.2 - - + -
204C GLY* 4.1 3.5 + - - -
446C PHE* 4.3 27.3 - + + -
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Residues in contact with LEU 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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127C ARG* 3.0 44.0 + - + -
128C ASP* 3.8 29.6 - - - +
129C PRO* 4.1 11.0 - - + -
154C PHE* 3.5 31.0 - - + -
168C GLN* 5.8 3.4 - - - +
186C TRP* 4.2 17.3 - - + -
195C GLN* 2.8 19.9 + - - +
196C VAL* 3.0 9.2 + - - +
198C PHE* 1.3 78.7 - - - +
200C PHE* 1.3 63.7 + - + +
204C GLY* 3.1 22.9 - - - +
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Residues in contact with PHE 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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127C ARG* 3.8 26.5 - - + +
183C TRP* 3.9 12.6 - + - -
186C TRP* 3.7 29.8 - + - -
196C VAL* 2.9 36.2 + - + +
199C LEU* 1.3 81.1 - - + +
201C SER* 1.3 60.7 + - - +
459C LEU* 3.6 16.4 - - + +
462C ASN* 3.2 55.0 + - + +
463C ILE* 3.6 24.2 - - + -
466C HIS* 3.6 32.1 - + + -
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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
----------------------------------------------------------
127C ARG* 3.0 17.8 + - - -
197C SER 3.3 12.8 + - - -
198C PHE* 3.1 19.7 + - - -
200C PHE* 1.3 83.4 - - - +
202C ASP* 1.3 68.8 + - - +
203C ARG* 3.1 19.6 + - - +
204C GLY 3.1 4.0 + - - -
446C PHE* 4.7 5.3 - - - -
451C LEU* 4.5 20.9 - - - -
455C GLN 5.9 0.4 - - - -
459C LEU* 4.3 8.1 - - - +
462C ASN* 4.7 2.8 + - - +
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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