Contacts of the strand formed by residues 197 - 213 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186D PHE* 3.4 2.5 - - - -
187D GLU* 2.8 79.5 + - + +
189D THR* 4.3 12.9 + - + +
194D GLN* 5.5 10.1 - - + +
195D GLY 3.1 6.8 + - - +
196D PRO* 1.3 72.4 - - - +
198D PRO* 1.3 71.5 - - + +
199D VAL* 3.7 11.1 + - + -
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Residues in contact with PRO 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D THR* 4.8 9.9 - - + -
185D LEU 3.6 8.5 - - - +
186D PHE* 4.0 22.2 - - + -
196D PRO 4.2 3.1 - - - +
197D LYS* 1.3 88.9 - - + +
199D VAL* 1.3 66.8 + - - +
133L HIS* 5.3 3.8 - - - +
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Residues in contact with VAL 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D PHE* 4.4 18.6 - - + -
183D LYS 3.8 0.2 - - - +
184D THR* 3.5 4.1 - - - +
185D LEU* 2.9 52.5 + - + +
187D GLU* 4.2 20.0 - - + +
197D LYS* 4.0 20.2 - - + +
198D PRO* 1.3 81.9 - - - +
200D THR* 1.3 64.6 + - - +
201D ILE* 4.2 12.7 + - + -
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Residues in contact with THR 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D SER* 4.0 26.0 - - - +
183D LYS 3.3 13.5 - - - +
184D THR* 3.7 17.2 + - - +
199D VAL* 1.3 74.7 - - - +
201D ILE* 1.3 70.2 + - - +
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Residues in contact with ILE 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D VAL* 4.2 22.7 - - + -
144D PHE* 3.2 37.9 - - + -
152D PHE* 4.4 17.5 - - + -
182D SER* 4.4 1.6 - - - -
183D LYS 3.0 28.5 + - - -
185D LEU* 4.5 5.4 - - + -
199D VAL* 4.5 13.5 - - + -
200D THR* 1.3 83.3 - - - +
202D SER* 1.3 65.3 + - - +
203D PHE* 3.3 21.6 - - + -
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Residues in contact with SER 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D PHE* 3.3 23.7 - - - -
180D TYR* 4.2 27.2 - - - +
181D LEU 3.2 8.6 + - - -
182D SER* 3.5 19.2 + - - -
201D ILE* 1.3 73.1 - - - +
203D PHE* 1.3 60.6 + - - +
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Residues in contact with PHE 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D ILE* 4.8 3.4 - - + -
140D VAL* 3.7 35.7 - - + -
143D GLU* 4.4 14.6 - - + -
144D PHE* 3.5 25.4 - + - -
157D VAL* 3.7 28.9 - - + -
159D VAL* 4.1 18.8 - - + -
161D ARG* 4.3 3.6 - - - +
180D TYR* 3.3 7.0 - - - -
181D LEU* 2.9 35.0 + - - +
183D LYS* 4.1 9.2 - - + -
185D LEU* 3.9 14.1 - - + -
201D ILE* 3.3 39.7 - - + -
202D SER* 1.3 74.5 - - - +
204D ALA* 1.3 63.8 - - - +
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Residues in contact with ALA 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D GLU* 4.7 2.1 + - - +
159D VAL* 3.7 8.7 - - - +
161D ARG* 2.9 39.7 + - - +
178D THR* 4.0 8.3 - - - +
179D SER 3.5 5.2 - - - -
180D TYR* 3.7 17.6 - - + -
203D PHE* 1.3 73.9 - - - +
205D ASN* 1.3 59.0 + - - +
206D HIS* 4.5 2.2 - - + -
1K NAG 3.7 31.9 - - - +
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Residues in contact with ASN 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D VAL* 3.8 4.4 - - + -
160D TYR* 2.8 30.6 + - - +
178D THR* 2.6 16.7 + - - -
179D SER* 2.7 33.1 + - - +
181D LEU* 3.7 26.2 - - + +
203D PHE 3.6 0.2 + - - -
204D ALA* 1.3 74.0 - - - +
206D HIS* 1.3 61.7 + - - +
207D THR* 3.5 7.4 + - - +
1P NAG 1.5 60.5 + - - +
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Residues in contact with HIS 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D PRO* 3.4 11.1 - - + +
160D TYR* 2.9 16.2 + - - +
161D ARG* 3.4 27.0 + - + -
162D CYS* 2.9 44.1 + - + +
175D ASN* 3.4 33.6 - - + +
177D SER 3.9 1.3 - - - -
178D THR* 3.5 14.8 - - - -
204D ALA* 4.5 3.1 - - + -
205D ASN* 1.3 69.6 - - - +
207D THR* 1.3 54.3 + - - +
208D SER 3.6 0.2 - - - -
209D CYS* 4.8 0.4 - - - -
1K NAG 3.2 30.9 + - - -
1P NAG 2.6 25.3 + - - +
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Residues in contact with THR 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D PRO* 4.0 5.6 - - - +
177D SER* 2.7 34.2 + - - -
178D THR* 3.7 3.0 + - - -
179D SER* 4.1 17.5 - - - -
205D ASN* 3.5 13.2 + - - +
206D HIS* 1.3 76.8 - - - +
208D SER* 1.3 63.3 + - - +
1P NAG 2.9 27.3 + - - +
2P NAG 5.8 0.5 - - - +
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Residues in contact with SER 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D PRO* 4.1 5.3 - - - +
162D CYS* 3.7 0.7 - - - -
175D ASN* 3.3 7.3 - - - +
176D THR* 2.7 47.6 + - - -
177D SER* 2.6 27.7 + - - -
206D HIS 3.6 1.0 - - - -
207D THR* 1.3 81.5 - - - +
209D CYS* 1.3 63.5 + - - +
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Residues in contact with CYS 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D CYS* 3.4 23.5 - - - +
132D MET* 3.4 9.2 - - - -
133D PRO* 3.3 32.3 - - - +
162D CYS* 2.0 46.4 - - - -
174D MET 3.3 6.3 - - - +
176D THR* 3.9 4.9 + - - -
208D SER* 1.3 76.9 - - - +
210D ARG* 1.3 65.0 + - - +
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Residues in contact with ARG 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D CYS* 3.8 6.5 - - - -
174D MET 3.0 25.7 + - - +
176D THR* 3.4 29.5 - - + +
209D CYS* 1.3 78.9 - - - +
211D CYS* 1.3 74.3 + - - +
212D MET* 3.2 35.0 + - - +
168O LYS* 5.3 11.2 - - - +
194O TYR* 6.6 0.4 - - + -
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Residues in contact with CYS 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D CYS* 3.8 22.4 - - - +
165D CYS 4.4 1.1 - - - -
166D CYS* 2.0 56.8 - - + -
167D ASN* 4.9 1.1 - - - +
171D LEU* 4.2 13.7 - - + +
172D GLN 3.4 5.4 - - - -
210D ARG* 1.3 81.7 + - - +
212D MET* 1.3 60.5 + - - +
194O TYR* 5.5 14.6 - - + +
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Residues in contact with MET 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D LEU* 3.2 8.3 - - - -
172D GLN* 2.7 38.4 + - - +
174D MET* 3.6 38.2 - - + +
175D ASN 5.3 3.4 - - - +
176D THR* 4.3 11.9 - - - -
210D ARG* 3.2 53.2 - - - +
211D CYS* 1.3 71.7 - - - +
213D SER* 1.3 71.3 + - - +
214D LYS* 3.5 0.5 + - - -
215D LEU* 6.6 0.7 - - + -
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Residues in contact with SER 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D GLY 3.6 10.3 - - - -
171D LEU* 3.4 11.6 - - - +
174D MET* 4.7 1.4 - - - +
212D MET* 1.3 83.5 - - - +
214D LYS* 1.3 65.1 - - - +
215D LEU* 3.1 28.6 + - - +
284O GLU* 6.0 5.6 - - - -
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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