Contacts of the strand formed by residues 197 - 213 (chain B) in PDB entry 2X1W
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186B PHE* 3.4 3.3 - - - -
187B GLU* 2.7 71.3 + - + +
189B THR* 4.4 11.8 + - - +
194B GLN* 2.9 37.2 - - - +
195B GLY 4.2 6.3 - - - +
196B PRO* 1.3 74.4 - - - +
198B PRO* 1.3 73.7 - - + +
199B VAL* 3.5 4.1 + - + +
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Residues in contact with PRO 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ILE* 4.4 15.5 - - + -
184B THR* 4.6 5.6 - - + -
185B LEU 3.4 9.0 - - - +
186B PHE* 3.6 22.7 - - + -
196B PRO 4.4 1.6 - - - +
197B LYS* 1.3 88.6 - - + +
199B VAL* 1.3 63.9 + - - +
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Residues in contact with VAL 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B PHE* 4.2 8.7 - - + -
183B LYS 3.9 0.7 - - - +
184B THR* 3.4 4.7 - - - -
185B LEU* 2.8 53.4 + - + +
187B GLU* 3.1 42.8 - - + +
197B LYS* 4.1 6.7 - - + +
198B PRO* 1.3 80.1 - - - +
200B THR* 1.3 63.2 + - - +
201B ILE* 4.0 9.3 + - + -
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Residues in contact with THR 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B SER* 3.9 25.1 - - - +
183B LYS 3.5 9.0 - - - +
184B THR* 3.1 17.6 + - - +
199B VAL* 1.3 72.8 - - - +
201B ILE* 1.3 67.8 + - - +
202B SER* 5.6 0.7 - - - +
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Residues in contact with ILE 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B VAL* 4.0 14.1 - - + -
144B PHE* 3.8 25.6 - - + -
152B PHE* 3.8 30.7 - - + -
181B LEU 3.5 1.0 - - - +
182B SER* 3.6 1.8 - - - -
183B LYS 2.9 31.7 + - - +
185B LEU* 4.3 9.2 - - + -
199B VAL* 4.4 13.7 - - + +
200B THR* 1.3 81.5 - - - +
202B SER* 1.3 65.3 + - - +
203B PHE* 3.7 27.1 - - + -
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Residues in contact with SER 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B PHE* 3.5 20.6 - - - -
180B TYR* 4.8 20.2 - - - +
181B LEU 3.2 8.4 + - - -
182B SER* 3.7 17.0 + - - -
200B THR* 5.6 0.5 - - - +
201B ILE* 1.3 73.9 - - - +
203B PHE* 1.3 62.1 + - - +
204B ALA 4.3 0.2 + - - -
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Residues in contact with PHE 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B ILE* 4.8 5.8 - - + -
140B VAL* 3.7 33.4 - - + -
143B GLU* 4.5 9.2 - - - -
144B PHE* 3.4 31.0 - + - -
157B VAL* 3.8 31.0 - - + -
159B VAL* 4.1 18.3 - - + +
161B ARG* 4.4 3.4 - - - +
180B TYR* 3.6 4.9 - - - -
181B LEU* 3.0 33.2 + - + +
183B LYS* 4.0 23.6 - - + -
185B LEU* 5.2 3.4 - - + -
201B ILE* 3.7 36.8 - - + -
202B SER* 1.3 73.0 - - - +
204B ALA* 1.3 65.1 + - - +
205B ASN* 3.5 0.7 + - - -
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Residues in contact with ALA 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B GLU* 4.8 2.3 + - - +
159B VAL* 3.8 8.7 - - - +
161B ARG* 2.8 42.3 + - - +
178B THR* 3.7 15.7 - - + -
179B SER 3.8 5.2 - - - -
180B TYR* 3.8 15.5 - - + -
203B PHE* 1.3 72.3 - - - +
205B ASN* 1.3 58.6 + - - +
206B HIS* 4.4 1.3 - - + -
1G NAG 3.7 27.8 - - - +
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Residues in contact with ASN 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B VAL* 4.1 1.5 - - + -
160B TYR* 3.1 26.0 + - - +
178B THR* 3.7 2.0 - - - -
179B SER* 2.8 39.0 + - - +
181B LEU* 3.9 27.8 - - + +
203B PHE 3.5 0.4 + - - -
204B ALA* 1.3 72.3 - - - +
206B HIS* 1.3 66.1 + - - +
207B THR* 3.3 7.5 + - - +
1H NAG 1.5 58.5 + - - +
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Residues in contact with HIS 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B PRO* 3.7 14.2 - - + +
160B TYR* 3.1 13.7 + - - +
161B ARG* 3.3 28.6 + - + -
162B CYS* 3.1 42.6 + - + +
175B ASN* 3.4 31.1 - - + +
177B SER 3.9 5.2 - - - -
178B THR* 3.8 9.6 - - + -
204B ALA* 4.4 1.6 - - + -
205B ASN* 1.3 71.9 - - - +
207B THR* 1.3 59.7 + - - +
208B SER 3.7 0.2 - - - -
209B CYS* 4.9 0.7 - - - -
1G NAG 3.0 38.2 + - - -
1H NAG 3.6 11.4 - - - +
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Residues in contact with THR 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B PRO* 4.0 10.6 - - - +
177B SER* 2.8 32.0 + - - -
178B THR* 4.1 2.3 + - - -
179B SER* 4.0 14.6 + - - -
205B ASN* 3.3 27.3 + - - +
206B HIS* 1.3 74.6 - - - +
208B SER* 1.3 63.5 + - - +
1H NAG 3.8 20.5 + - - +
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Residues in contact with SER 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B PRO* 4.2 4.0 - - - +
162B CYS* 3.7 0.5 - - - -
175B ASN* 3.4 6.9 - - - +
176B THR* 2.7 45.5 + - - -
177B SER* 2.7 25.0 + - - -
206B HIS 3.7 0.8 - - - -
207B THR* 1.3 83.1 + - - +
209B CYS* 1.3 66.2 + - - +
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Residues in contact with CYS 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B CYS* 3.5 23.5 - - - +
132B MET* 3.4 6.7 - - - +
133B PRO* 3.3 35.7 - - - +
162B CYS* 2.0 44.4 - - - -
174B MET 3.1 6.5 - - - +
176B THR* 4.2 3.8 - - - -
208B SER* 1.3 77.7 - - - +
210B ARG* 1.3 64.5 + - - +
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Residues in contact with ARG 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B CYS* 3.8 7.4 - - - -
174B MET 2.9 25.7 + - - +
176B THR* 3.8 33.4 + - + +
209B CYS* 1.3 76.9 - - - +
211B CYS* 1.3 74.0 + - - +
212B MET* 3.2 22.6 + - + +
235O GLU* 4.5 12.7 + - - +
237O SER* 5.4 4.5 + - - -
240O GLU* 4.8 12.3 + - - -
325O HIS* 3.5 34.6 + - - -
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Residues in contact with CYS 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B CYS* 3.7 21.8 - - - +
165B CYS 4.6 0.9 - - - -
166B CYS* 2.0 55.0 - - + -
167B ASN 5.1 0.2 - - - -
171B LEU* 4.1 19.6 - - + +
172B GLN 3.7 4.7 - - - -
210B ARG* 1.3 80.5 - - - +
212B MET* 1.3 61.6 + - - +
194M TYR* 5.5 12.8 - - + +
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Residues in contact with MET 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B LEU* 3.8 6.1 - - - -
172B GLN* 2.7 40.2 + - - +
174B MET* 3.4 35.1 - - + +
175B ASN 5.2 2.2 - - - +
176B THR* 4.1 25.1 - - - -
210B ARG* 3.2 24.2 + - + +
211B CYS* 1.3 77.7 - - - +
213B SER* 1.3 63.2 + - - +
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Residues in contact with SER 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B GLY 3.3 17.3 - - - -
171B LEU* 3.7 12.2 - - - +
174B MET* 3.9 12.0 - - - +
212B MET* 1.3 79.5 - - - +
214B LYS* 1.3 66.6 + - - +
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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