Contacts of the strand formed by residues 204 - 216 (chain E) in PDB entry 1PPE
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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121E ILE* 4.4 1.1 - - - -
122E SER* 3.4 27.2 + - - +
123E LEU 4.0 11.8 + - - +
124E PRO* 3.9 26.9 - - + -
125E THR* 5.0 11.8 - - - +
200E VAL* 3.4 5.4 - - - +
201E CYS 2.9 27.2 + - - +
202E SER* 3.7 14.6 - - - +
203E GLY* 1.3 87.6 - - - +
209E LEU* 1.3 59.7 + - - +
210E GLN* 3.1 14.0 + - - +
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Residues in contact with LEU 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E SER* 3.6 24.2 - - - +
47E ILE* 4.3 10.5 - - + -
53E VAL* 3.4 32.5 - - + -
121E ILE* 4.0 9.9 - - + +
122E SER 2.8 19.2 + - - +
123E LEU* 4.5 4.7 - - + -
124E PRO* 3.2 21.4 - - - +
198E PRO* 3.7 18.8 - - + -
199E VAL 3.8 6.1 - - - +
200E VAL* 4.2 5.4 - - + -
204E LYS* 1.3 69.4 - - - +
210E GLN* 1.3 58.2 + - - +
211E GLY 3.4 23.1 - - - +
212E ILE* 5.3 1.3 - - + -
231E VAL* 3.5 22.0 - - + +
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Residues in contact with GLN 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E PRO* 3.4 22.4 - - - +
127E SER 3.1 25.3 + - - +
128E CYS* 3.8 0.4 - - - +
129E ALA* 3.7 30.0 - - + +
162E ILE* 5.0 0.7 - - + -
181E PHE* 3.4 16.9 - - + -
199E VAL 3.0 5.9 + - - -
201E CYS* 3.7 38.0 - - + +
204E LYS* 3.1 11.1 + - - +
209E LEU* 1.3 74.1 - - - +
211E GLY* 1.3 57.8 + - - +
230E LYS* 4.0 1.0 - - - +
231E VAL* 3.1 24.4 + - - -
232E CYS* 3.8 13.5 - - - +
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Residues in contact with GLY 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181E PHE* 3.7 10.3 - - - -
198E PRO 3.8 0.3 - - - -
199E VAL* 3.0 41.0 + - - +
209E LEU* 3.4 13.9 - - - +
210E GLN* 1.3 77.8 - - - +
212E ILE* 1.3 63.8 + - - +
228E TYR* 4.6 0.4 - - - -
229E THR 3.2 9.4 - - - -
231E VAL* 3.8 1.3 - - - +
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Residues in contact with ILE 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E VAL* 3.7 19.3 - - + -
54E SER 3.6 16.2 - - - +
55E ALA* 3.6 16.6 - - + +
102E ASP 4.2 5.4 - - - +
103E ILE* 3.7 31.0 - - + -
196E GLY* 3.5 34.1 - - - +
197E GLY 3.4 4.9 - - - +
209E LEU* 5.3 1.6 - - + -
211E GLY* 1.3 75.4 - - - +
213E VAL* 1.3 69.2 + - - +
214E SER* 3.9 0.7 - - - -
228E TYR* 3.1 8.3 - - - -
229E THR* 2.9 35.6 + - - +
231E VAL* 3.6 14.4 - - + -
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Residues in contact with VAL 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E ALA* 4.0 3.5 - - - +
138E ILE* 3.9 20.9 - - + -
139E SER 5.0 1.3 - - - +
190E SER* 3.6 21.1 - - - +
194E ASP* 3.3 40.2 - - + +
195E SER* 3.6 6.8 + - - +
196E GLY* 2.9 24.3 + - - +
197E GLY* 2.9 24.1 + - - +
199E VAL* 4.5 1.8 - - + +
211E GLY 4.3 0.2 - - - -
212E ILE* 1.3 72.5 - - - +
214E SER* 1.3 63.8 + - - +
228E TYR* 3.6 22.5 - - + -
5I ARG* 4.1 12.1 - - - -
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Residues in contact with SER 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E HIS* 3.2 15.1 + - - -
99E LEU* 4.5 1.9 + - - +
102E ASP* 2.6 30.3 + - - +
195E SER* 4.3 0.4 - - - -
212E ILE 3.2 7.8 + - - -
213E VAL* 1.3 80.0 - - - +
215E TRP* 1.3 78.6 + - - +
227E VAL 3.1 17.6 + - - -
228E TYR 4.5 0.7 - - - -
229E THR* 3.9 13.0 - - - -
4I PRO* 3.3 0.3 - - - +
5I ARG* 3.1 24.6 + - - +
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Residues in contact with TRP 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E THR 4.9 2.0 - - - -
99E LEU* 3.4 30.8 - - + +
172E TYR* 3.7 41.5 - + - -
175E GLN* 3.9 29.8 - - + -
176E ILE* 3.9 20.2 - - + -
180E MET* 3.9 16.6 - - + +
214E SER* 1.3 96.5 - - - +
216E GLY* 1.3 72.0 + - - +
226E GLY 3.8 0.5 - - - -
227E VAL* 2.8 54.8 + - + +
1I ARG 4.0 1.8 - - - -
2I VAL* 3.8 37.7 - - + -
3I CYS 3.4 15.9 - - - +
4I PRO* 3.7 1.1 - - + -
5I ARG* 3.6 14.9 + - - +
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Residues in contact with GLY 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172E TYR* 3.6 12.1 - - - -
192E GLN* 5.5 0.3 + - - -
215E TRP* 1.3 81.2 - - - +
217E SER* 1.3 61.5 + - - -
219E GLY 3.8 5.3 + - - +
225E PRO 4.3 2.5 - - - -
227E VAL 4.8 0.2 - - - -
1I ARG 3.3 11.9 - - - +
3I CYS* 3.3 20.8 + - - +
5I ARG* 3.5 19.4 - - - +
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Residues in contact with SER 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172E TYR* 3.2 22.6 + - - -
216E GLY* 1.3 71.8 - - - -
219E GLY* 1.3 60.7 + - - +
220E CYS 3.8 0.7 + - - -
221E GLN* 4.0 8.5 - - - +
224E LYS* 3.7 34.8 - - - +
1I ARG* 2.8 46.8 + - - +
3I CYS* 5.4 0.2 - - - -
5I ARG* 4.6 0.2 - - - +
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Residues in contact with GLY 219 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192E GLN* 4.8 4.4 + - - -
216E GLY 3.8 4.8 + - - +
217E SER* 1.3 72.9 - - - +
220E CYS* 1.3 69.3 + - - -
221E GLN* 3.8 8.3 - - - -
1I ARG* 3.7 22.4 - - - +
3I CYS* 5.3 1.6 - - - +
5I ARG* 3.1 20.7 + - - -
29I GLY* 4.6 8.4 + - - -
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Residues in contact with CYS 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E VAL* 4.0 9.4 - - + -
146E SER* 3.2 16.4 + - - +
189E ASP* 3.7 5.4 - - - -
190E SER 3.9 5.2 - - - +
191E CYS* 2.0 59.0 - - + -
192E GLN* 3.3 14.6 - - - -
217E SER 5.1 0.2 - - - -
219E GLY* 1.3 80.2 - - - -
221E GLN* 1.3 93.6 + - - +
5I ARG* 4.6 0.9 - - - -
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Residues in contact with ALA 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E VAL* 3.9 19.5 - - + -
146E SER* 4.0 5.8 - - - -
187E GLY* 3.1 5.6 - - - -
188E GLY* 2.8 49.9 + - - +
189E ASP* 2.8 36.4 + - + +
220E CYS* 1.3 75.4 - - - +
221E GLN* 1.3 64.7 + - - +
222E LYS 3.8 0.3 + - - -
224E LYS 4.8 0.6 + - - -
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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