Contacts of the strand formed by residues 204 - 217 (chain C) in PDB entry 4B2B
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 LYS 204 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122C SER* 3.4 19.3 + - - +
123C LEU 3.6 18.5 + - - +
124C PRO* 4.2 11.4 - - + -
125C THR* 5.0 18.6 - - - +
200C VAL* 3.2 5.8 - - - +
201C CYS 2.8 32.4 + - - +
202C SER* 4.0 11.9 - - - +
203C GLY* 1.3 85.6 + - - +
209C LEU* 1.3 59.5 + - - +
210C GLN* 3.1 25.1 + - - +
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Residues in contact with LEU 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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45C SER* 3.6 37.0 - - - +
47C ILE* 4.1 18.2 - - + -
53C VAL* 4.2 19.7 - - + -
121C ILE* 4.1 11.2 - - + +
122C SER 2.9 18.5 + - - +
123C LEU* 4.3 9.4 - - + -
124C PRO* 3.1 21.5 - - - +
198C PRO* 3.7 15.5 - - + -
199C VAL 3.7 4.3 - - - +
200C VAL* 4.1 6.7 - - + -
204C LYS* 1.3 70.2 - - - +
210C GLN* 1.3 57.3 + - - +
211C GLY 3.5 23.8 - - - +
212C ILE* 5.3 1.1 - - + -
231C VAL* 3.3 12.4 - - + +
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Residues in contact with GLN 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C PRO* 3.4 24.1 - - - +
127C SER 3.1 23.1 + - - +
128C CYS 4.0 0.6 - - - -
129C ALA* 3.7 30.9 + - + +
162C ILE* 5.1 0.4 - - + -
181C PHE* 3.3 18.1 - - + -
199C VAL 2.9 5.7 + - - -
201C CYS* 3.9 30.7 + - + +
204C LYS* 3.1 23.6 + - + +
209C LEU* 1.3 73.6 - - - +
211C GLY* 1.3 58.4 + - - +
230C LYS* 3.9 1.6 - - - +
231C VAL* 3.0 24.9 + - - -
232C CYS* 3.9 10.0 + - - +
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Residues in contact with GLY 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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181C PHE* 3.7 10.3 - - - -
198C PRO* 3.7 0.3 - - - +
199C VAL* 2.9 40.7 + - - +
209C LEU* 3.5 13.9 - - - +
210C GLN* 1.3 80.7 - - - +
212C ILE* 1.3 66.0 + - - +
228C TYR* 4.4 0.2 - - - -
229C THR 3.2 8.7 - - - -
231C VAL* 3.8 1.3 - - - -
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Residues in contact with ILE 212 (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 VAL* 3.5 30.7 - - + -
54C SER 3.6 3.6 - - - +
55C ALA* 3.9 14.4 - - + +
102C ASP 4.1 5.4 - - - +
103C ILE* 3.5 31.6 - - + -
196C GLY* 3.6 31.2 - - - +
197C GLY 3.3 4.7 - - - +
209C LEU* 5.3 2.5 - - + -
211C GLY* 1.3 77.9 - - - +
213C VAL* 1.3 71.5 + - - +
214C SER* 3.2 1.7 + - - -
228C TYR* 3.2 5.6 - - - +
229C THR* 2.9 36.0 + - - +
231C VAL* 3.7 14.6 - - + -
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Residues in contact with VAL 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ALA* 4.0 2.8 - - - +
138C ILE* 3.9 20.0 - - + -
139C SER 4.8 1.8 - - - +
190C ALA* 3.7 22.9 - - + -
194C ASP* 3.3 38.8 - - + +
195C ALA* 3.4 6.9 - - - +
196C GLY 2.8 24.7 + - - +
197C GLY* 2.9 18.2 + - - +
198C PRO 4.5 1.1 - - - +
199C VAL* 4.6 0.6 - - + +
212C ILE* 1.3 72.8 - - - +
214C SER* 1.3 59.9 + - - +
228C TYR* 3.6 22.3 - - + -
45D LYS* 4.1 13.5 - - + -
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Residues in contact with SER 214 (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 ALA* 5.7 0.2 - - - -
57C HIS* 3.3 11.8 - - - -
99C TYR* 4.5 1.6 + - - +
102C ASP* 2.6 32.0 + - - +
180C MET* 6.5 0.4 - - - -
212C ILE 3.2 2.9 + - - -
213C VAL* 1.3 76.6 - - - +
215C TRP* 1.3 79.6 + - - +
227C PHE 3.2 14.0 + - - -
228C TYR* 4.1 1.1 - - - -
229C THR* 3.7 21.8 - - - -
44D THR* 3.5 0.9 - - - -
45D LYS* 3.0 26.2 + - - +
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Residues in contact with TRP 215 (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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99C TYR* 3.4 33.2 - + + -
172C SER* 3.9 5.2 - - - -
174C PHE* 3.4 30.5 - + + -
176C ILE* 4.6 3.8 - - + -
180C MET* 3.5 30.4 - - + +
214C SER* 1.3 103.0 - - - +
216C GLY* 1.3 79.2 + - - +
217C GLU* 4.6 4.5 - - + -
227C PHE* 2.9 83.2 + + + +
228C TYR 5.3 0.2 - - - -
42D PRO* 3.6 30.5 - - + -
43D VAL 3.2 17.0 - - - +
44D THR* 4.1 2.5 - - + -
45D LYS* 3.8 13.5 - - - +
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Residues in contact with GLY 216 (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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215C TRP* 1.3 87.5 - - - +
217C GLU* 1.3 63.8 + - - -
219C GLY 3.6 9.2 + - - +
224C LYS 6.1 0.2 - - - -
225C PRO 5.0 0.7 - - - -
226C GLY* 4.9 2.9 - - - -
227C PHE* 4.7 5.8 - - - -
43D VAL* 2.9 35.1 + - - +
45D LYS* 3.7 13.2 - - - +
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Residues in contact with GLU 217 (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 SER* 3.9 7.1 + - - -
173C SER* 2.4 35.9 + - - -
174C PHE* 3.6 12.5 + - - +
215C TRP* 4.6 4.9 - - + -
216C GLY* 1.3 67.4 - - - -
219C GLY* 1.3 63.6 + - - +
221C GLN* 4.3 5.5 - - - +
224C LYS* 2.8 67.1 + - + +
225C PRO 5.4 2.6 + - - -
227C PHE* 5.7 1.7 - - + -
40D GLY* 3.3 23.8 - - - +
41D SER 3.7 6.5 - - - -
42D PRO* 3.8 16.9 - - + +
1073D GOL 4.7 2.2 - - - -
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Residues in contact with GLY 219 (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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189C ASP* 4.4 1.9 - - - +
192C GLN* 5.5 2.2 + - - -
216C GLY* 3.6 15.3 + - - +
217C GLU* 1.3 76.7 - - - +
220C CYS* 1.3 70.7 + - - -
221C GLN* 4.6 6.7 - - - -
224C LYS 5.4 0.3 - - - +
41D SER 4.3 2.6 + - - -
43D VAL* 5.1 4.8 - - - +
45D LYS* 4.1 8.1 - - - -
1073D GOL 3.9 23.8 + - - -
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Residues in contact with CYS 220 (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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17C VAL* 4.2 9.2 - - + -
146C SER* 3.3 15.2 + - - +
189C ASP* 3.6 4.9 - - - -
190C ALA 3.8 5.4 - - - +
191C CYS* 2.1 57.0 - - + -
192C GLN* 3.4 15.7 - - - -
217C GLU 3.9 0.2 + - - -
219C GLY* 1.3 79.9 - - - -
221C GLN* 1.3 89.2 + - - +
45D LYS* 4.6 1.8 - - - -
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Residues in contact with ALA 221 (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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17C VAL* 3.8 20.6 - - + -
146C SER* 4.3 4.4 - - - -
187C GLY* 3.4 2.2 - - - -
188C GLY* 2.9 50.9 + - - +
189C ASP* 2.8 29.8 + - + +
220C CYS* 1.3 73.3 - - - +
221C GLN* 1.3 66.0 + - - +
222C LYS 3.9 0.2 + - - -
224C LYS 4.8 0.6 + - - -
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Residues in contact with GLN 221 (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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146C SER* 3.7 22.6 - - - -
184C TYR 4.7 2.3 - - - +
187C GLY* 3.9 6.0 - - - -
217C GLU 4.3 6.1 - - - +
219C GLY* 4.6 4.0 - - - -
220C CYS* 3.0 31.8 - - - +
221C ALA* 1.3 82.1 - - - +
222C LYS* 1.4 67.8 + - - +
223C ASN 3.3 0.9 + - - -
224C LYS* 3.1 38.7 + - + +
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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