Contacts of the strand formed by residues 197 - 213 (chain E) in PDB entry 2X1X
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 197 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186E PHE* 3.5 2.0 - - - -
187E GLU* 3.0 63.2 + - + +
189E THR* 3.9 15.1 + - - +
194E GLN* 3.5 29.4 - - + +
195E GLY 3.2 3.5 + - - +
196E PRO* 1.3 73.2 - - - +
198E PRO* 1.3 67.2 - - + +
199E VAL* 3.1 19.7 + - + +
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Residues in contact with PRO 198 (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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184E THR* 4.3 16.2 - - + -
185E LEU 3.8 5.8 - - - +
186E PHE* 3.7 24.4 - - + -
196E PRO 4.0 5.6 - - - +
197E LYS* 1.3 83.5 - - + +
199E VAL* 1.3 61.3 + - - +
200E THR* 5.7 0.7 - - - +
133R HIS* 6.0 1.3 - - + +
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Residues in contact with VAL 199 (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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152E PHE* 4.2 14.6 - - + -
183E LYS 4.0 0.2 - - - +
184E THR* 3.4 2.3 - - - -
185E LEU* 2.8 45.9 + - - +
187E GLU* 3.6 32.3 - - + +
197E LYS* 3.1 23.3 + - + +
198E PRO* 1.3 78.8 - - - +
200E THR* 1.3 65.0 + - - +
201E ILE* 4.7 8.7 - - + -
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Residues in contact with THR 200 (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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144E PHE* 5.8 1.2 - - - -
182E SER* 4.9 13.2 - - - -
183E LYS 3.2 7.9 - - - +
184E THR* 3.2 28.5 - - + +
198E PRO 5.7 0.7 - - - +
199E VAL* 1.3 76.0 - - - +
201E ILE* 1.3 68.8 + - - +
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Residues in contact with ILE 201 (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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140E VAL* 3.6 26.9 - - + -
144E PHE* 3.7 41.5 - - + -
152E PHE* 3.7 25.8 - - + -
181E LEU 3.4 1.7 - - - +
182E SER* 3.4 2.6 - - - -
183E LYS 2.9 30.0 + - - +
185E LEU* 3.9 13.5 - - + -
199E VAL* 4.7 6.7 - - + -
200E THR* 1.3 81.1 - - - +
202E SER* 1.3 67.1 + - - +
203E PHE* 3.5 30.8 - - + -
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Residues in contact with SER 202 (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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180E TYR* 3.8 29.3 - - - +
181E LEU 3.1 9.1 + - - -
182E SER* 4.2 6.3 - - - +
201E ILE* 1.3 77.8 - - - +
203E PHE* 1.3 61.9 + - - +
204E ALA 4.1 0.9 + - - -
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Residues in contact with PHE 203 (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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138E ILE* 4.3 14.8 - - + -
140E VAL* 3.6 41.1 - - + -
143E GLU* 4.8 16.8 - - + -
144E PHE 5.8 0.9 - - - -
157E VAL* 3.8 32.8 - - + -
159E VAL* 4.2 18.1 - - + +
161E ARG* 4.5 4.0 - - - +
180E TYR* 3.5 2.4 - - - -
181E LEU* 2.6 45.7 + - + +
183E LYS* 4.3 10.8 - - + -
185E LEU* 4.0 7.2 - - + -
201E ILE* 3.5 37.7 - - + -
202E SER* 1.3 75.2 - - - +
204E ALA* 1.3 63.0 + - - +
205E ASN* 3.6 0.5 + - - +
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Residues in contact with ALA 204 (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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1A NAG 3.7 31.6 - - - +
2A NAG 5.9 0.2 - - - +
143E GLU* 5.6 0.2 + - - -
159E VAL* 4.2 8.0 - - - +
161E ARG* 2.9 38.3 + - - +
178E THR* 3.8 6.1 - - + -
179E SER 3.6 5.2 - - - -
180E TYR* 3.8 19.9 - - + -
202E SER 4.1 0.6 + - - -
203E PHE* 1.3 73.2 - - - +
205E ASN* 1.3 58.4 + - - +
206E HIS* 4.7 1.3 - - - +
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Residues in contact with ASN 205 (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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1B NAG 3.0 40.9 + - - +
159E VAL* 4.4 5.3 - - + -
160E TYR* 3.2 29.7 + - - +
178E THR* 3.7 2.5 - - - -
179E SER* 2.6 48.7 + - - +
181E LEU* 3.3 33.2 - - + +
203E PHE 3.6 0.4 + - - +
204E ALA* 1.3 74.8 - - - +
206E HIS* 1.3 70.0 + - - +
207E THR* 3.8 0.3 - - - +
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Residues in contact with HIS 206 (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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1A NAG 3.7 20.5 + - - -
1B NAG 3.6 10.4 - - - -
133E PRO* 3.8 7.8 - - + +
160E TYR* 2.9 14.6 + - - +
161E ARG* 3.4 29.2 + - + -
162E CYS* 3.2 34.7 + - + +
175E ASN* 3.2 50.3 + - + +
177E SER 3.8 3.6 - - - -
178E THR* 3.5 12.6 - - + -
204E ALA* 4.7 0.8 - - + +
205E ASN* 1.3 85.4 + - - +
207E THR* 1.3 60.0 + - - +
208E SER 3.7 0.2 - - - -
209E CYS* 5.0 0.2 - - - -
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Residues in contact with THR 207 (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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1B NAG 3.2 34.6 + - - +
133E PRO* 4.0 8.2 - - - +
177E SER* 2.7 35.0 + - - -
178E THR* 4.3 0.5 + - - -
179E SER* 3.8 22.3 + - - +
205E ASN 3.8 9.9 - - - +
206E HIS* 1.3 77.0 - - - +
208E SER* 1.3 62.4 + - - +
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Residues in contact with SER 208 (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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133E PRO* 4.2 4.9 - - - +
175E ASN* 3.0 10.0 - - - +
176E THR* 2.7 49.0 + - - -
177E SER* 2.7 26.8 + - - -
206E HIS 3.7 0.4 - - - -
207E THR* 1.3 81.2 + - - +
209E CYS* 1.3 59.8 + - - +
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Residues in contact with CYS 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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131E CYS* 3.5 33.8 - - - +
132E MET* 3.4 1.3 - - - -
133E PRO* 3.3 34.3 - - - +
162E CYS* 2.0 46.2 - - - -
174E MET 3.3 6.5 - - - +
176E THR* 4.1 3.7 + - - -
208E SER* 1.3 75.0 - - - +
210E ARG* 1.3 65.2 + - - +
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Residues in contact with ARG 210 (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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131E CYS* 3.7 7.4 - - - -
174E MET 2.9 26.0 + - - +
176E THR* 3.6 35.1 + - + +
209E CYS* 1.3 77.7 + - - +
211E CYS* 1.3 66.9 + - - +
212E MET* 3.1 29.9 + - + +
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Residues in contact with CYS 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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131E CYS* 3.6 22.1 - - - +
165E CYS 4.3 1.3 - - - -
166E CYS* 2.0 55.0 - - + -
171E LEU* 3.7 23.8 - - + +
172E GLN 3.5 6.7 - - - -
210E ARG* 1.3 75.2 - - - +
212E MET* 1.3 62.2 + - - +
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Residues in contact with MET 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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1A NAG 6.4 0.9 - - + -
171E LEU* 4.0 2.5 - - - -
172E GLN* 3.1 28.5 + - - +
174E MET* 3.8 40.1 - - + +
175E ASN 4.2 6.1 - - - +
176E THR* 3.9 27.4 - - + -
210E ARG* 3.1 35.4 + - + +
211E CYS* 1.3 74.6 - - - +
213E SER* 1.3 68.7 + - - +
214E LYS* 4.4 0.3 - - - -
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Residues in contact with SER 213 (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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170E GLY 3.1 12.1 - - - -
171E LEU* 3.9 10.3 - - - +
174E MET* 4.5 8.3 - - - +
212E MET* 1.3 77.4 - - - +
214E LYS* 1.3 66.6 + - - +
215E LEU* 4.7 10.8 + - - -
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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