Contacts of the helix formed by residues 198 - 211 (chain C) in PDB entry 4QYJ
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 198 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32C LEU* 5.7 2.7 - - + -
34C VAL* 3.3 34.8 - - + -
46C VAL* 4.2 15.0 - - + -
103C ASN* 3.9 4.0 - - - +
193C PRO* 4.0 10.4 - - + +
194C ALA 4.0 9.0 - - - +
195C GLU* 4.1 4.7 - - - +
197C THR* 1.3 85.5 - - - +
199C LEU* 1.3 63.4 + - + +
200C THR 3.5 2.2 - - - -
201C ALA* 3.5 9.0 + - - +
202C LEU* 3.4 21.2 + - + +
222C THR* 3.7 27.6 - - + -
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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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34C VAL* 4.7 1.6 - - + -
43C LEU* 3.6 31.9 - - + -
44C THR* 3.9 26.7 - - + -
46C VAL* 4.1 17.5 - - + -
99C LEU* 3.8 31.1 - - + +
103C ASN* 3.9 15.3 + - + +
197C THR 3.8 0.8 - - - -
198C PRO* 1.3 76.2 - - + +
200C THR* 1.3 65.4 + - - +
202C LEU* 3.1 23.3 + - + +
203C ARG* 3.2 13.7 + - - +
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Residues in contact with THR 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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96C LEU* 4.2 15.2 - - + +
99C LEU* 4.2 28.5 - - + -
100C GLU* 3.4 37.2 + - - +
103C ASN* 5.1 2.6 + - + -
171C PRO* 3.5 17.2 - - - +
172C LEU* 4.2 21.7 - - + +
197C THR 5.0 0.5 + - - -
198C PRO 4.8 0.9 - - - -
199C LEU* 1.3 77.9 + - + +
201C ALA* 1.3 58.2 + - - +
203C ARG* 3.7 4.1 + - - +
204C LEU* 3.2 24.1 + - - +
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Residues in contact with ALA 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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166C ILE* 5.1 3.1 - - + -
171C PRO 5.3 1.7 + - - +
172C LEU* 6.0 0.2 - - - +
175C ALA* 4.7 10.1 - - + -
191C LEU* 3.9 21.9 - - + +
193C PRO* 3.9 31.2 - - + -
197C THR 5.7 0.4 + - - +
198C PRO 3.5 2.9 + - - +
199C LEU 3.3 0.6 - - - -
200C THR* 1.3 79.0 + - - +
202C LEU* 1.3 61.0 + - - +
203C ARG 3.3 0.2 - - - -
204C LEU* 3.4 10.5 - - - +
205C ALA* 3.0 27.5 + - - +
218C LEU* 5.9 0.2 - - - +
220C VAL* 4.1 7.2 - - + +
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Residues in contact with LEU 202 (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 GLN 3.4 32.1 - - - +
17C MET* 4.1 12.6 - - + -
23C TRP* 3.6 21.9 - - + -
46C VAL* 4.1 21.5 - - + -
198C PRO* 3.4 15.2 + - + +
199C LEU* 3.1 24.2 + - + +
201C ALA* 1.3 76.4 - - - +
203C ARG* 1.3 62.8 + - - +
205C ALA* 3.5 6.3 + - - +
206C GLU* 3.4 16.5 + - - +
220C VAL* 3.9 28.5 - - + -
222C THR* 4.9 4.7 - - + -
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Residues in contact with ARG 203 (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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92C HIS* 4.0 25.1 + - - +
95C GLU* 5.8 6.5 - - - +
96C LEU* 3.5 30.9 - - + +
99C LEU* 4.3 12.8 - - + -
199C LEU 3.2 13.4 + - - +
200C THR 4.0 1.3 - - - +
202C LEU* 1.3 73.9 - - - +
204C LEU* 1.3 65.5 + - - +
206C GLU* 2.8 47.6 + - - +
207C LEU* 3.1 50.2 + - + +
210C GLU* 5.0 4.0 + - - -
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Residues in contact with LEU 204 (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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85C LEU* 4.5 18.6 - - + -
89C LEU* 4.6 14.1 - - + -
96C LEU* 5.0 1.5 - - - +
123C LEU* 5.5 0.7 - - + -
172C LEU* 4.1 24.2 - - + -
175C ALA* 3.8 30.1 - - + -
176C VAL* 4.3 19.1 - - + +
179C ILE* 4.6 13.5 - - + -
191C LEU* 5.0 4.3 - - + -
200C THR 3.2 17.0 + - - +
201C ALA* 3.4 11.7 - - + +
202C LEU 3.3 0.2 - - - -
203C ARG* 1.3 75.4 - - - +
205C ALA* 1.3 56.8 + - - +
207C LEU* 3.2 9.7 + - - +
208C ALA* 2.8 29.4 + - - +
218C LEU* 5.0 8.3 - - + -
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Residues in contact with ALA 205 (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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18C LEU* 3.7 23.4 - - + +
23C TRP* 4.7 1.3 - - + -
201C ALA 3.0 6.6 + - - +
202C LEU* 3.6 9.9 - - - +
203C ARG 3.3 0.2 - - - -
204C LEU* 1.3 77.3 - - - +
206C GLU* 1.3 58.5 + - - +
208C ALA* 3.4 14.2 - - - +
209C MET* 3.4 15.4 + - - +
218C LEU* 3.8 17.1 - - + +
220C VAL* 3.4 31.6 - - + -
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Residues in contact with GLU 206 (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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18C LEU* 5.6 0.2 - - - -
23C TRP* 3.2 37.6 + - + +
202C LEU 3.4 6.6 + - - +
203C ARG* 2.8 41.0 + - - +
204C LEU 3.3 1.0 - - - -
205C ALA* 1.3 75.7 - - - +
207C LEU* 1.3 61.8 + - - +
208C ALA 3.2 0.2 - - - -
209C MET* 3.6 8.5 + - - +
210C GLU* 3.3 22.5 + - - +
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Residues in contact with LEU 207 (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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85C LEU* 3.2 21.6 - - + +
88C LEU* 3.6 29.7 - - + +
89C LEU* 3.7 20.2 - - + -
92C HIS* 3.5 28.3 - - + -
96C LEU* 4.1 12.8 - - + -
203C ARG* 3.1 40.7 + - + +
204C LEU* 3.6 5.2 - - - +
206C GLU* 1.3 72.4 - - - +
208C ALA* 1.3 65.7 + - - +
209C MET 3.2 0.4 - - - -
210C GLU* 3.7 17.5 - - - +
211C ALA* 3.1 18.5 + - - +
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Residues in contact with ALA 208 (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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81C ILE* 4.6 0.9 - - - +
85C LEU* 3.6 21.1 - - + +
179C ILE* 6.2 0.2 - - + -
183C LEU* 5.8 0.2 - - + -
204C LEU* 2.8 13.4 + - + +
205C ALA 3.4 11.4 - - - +
206C GLU 3.2 0.2 - - - -
207C LEU* 1.3 79.5 - - - +
209C MET* 1.3 60.2 + - + +
211C ALA* 3.4 9.4 + - - +
212C GLY 3.4 0.5 + - - -
213C LEU* 3.2 47.8 + - + +
218C LEU* 3.8 14.4 - - + -
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Residues in contact with MET 209 (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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18C LEU* 4.4 18.8 - - + -
21C GLY* 3.8 24.0 - - - +
23C TRP* 6.3 0.4 - - - -
205C ALA 3.4 13.8 + - - +
206C GLU* 3.6 9.4 + - - +
208C ALA* 1.3 77.5 - - + +
210C GLU* 1.3 63.7 + - - +
212C GLY* 3.2 13.7 + - - -
213C LEU* 3.8 18.9 + - + +
214C PRO 5.4 0.9 - - - +
215C ALA* 3.5 43.1 - - + +
216C GLY 5.7 0.2 - - - -
218C LEU 5.9 0.7 - - - +
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Residues in contact with GLU 210 (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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84C ARG* 5.0 4.2 + - - -
88C LEU* 3.7 31.3 - - + +
92C HIS* 4.0 9.5 + - - -
203C ARG* 5.0 4.7 + - - -
206C GLU* 3.3 14.1 + - - +
207C LEU* 3.4 23.5 + - - +
209C MET* 1.3 77.6 - - - +
211C ALA* 1.3 58.5 + - - +
212C GLY* 3.4 1.2 + - - -
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Residues in contact with ALA 211 (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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81C ILE* 3.6 32.9 - - + +
84C ARG* 3.5 32.5 + - + +
85C LEU* 3.7 21.8 - - + +
88C LEU* 3.9 4.2 - - + +
207C LEU 3.1 12.7 + - - +
208C ALA 3.5 10.8 - - - +
209C MET 3.2 0.2 - - - -
210C GLU* 1.3 77.9 - - - +
212C GLY* 1.3 55.8 + - - +
213C LEU 3.7 0.4 - - - -
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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