Contacts of the strand formed by residues 197 - 212 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A PHE* 3.4 3.3 - - - -
187A GLU* 2.7 66.5 + - + +
189A THR* 2.8 30.6 + - - +
194A GLN* 5.2 12.6 - - + -
195A GLY 4.0 8.5 - - - +
196A PRO* 1.3 73.1 - - - +
198A PRO* 1.3 74.5 - - + +
199A VAL* 3.5 4.0 + - + +
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Residues in contact with PRO 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A THR* 4.6 12.6 - - + -
185A LEU 3.4 8.5 - - - +
186A PHE* 3.6 23.3 - - + -
196A PRO 4.3 1.3 - - - +
197A LYS* 1.3 90.1 - - + +
199A VAL* 1.3 63.7 + - - +
118B ILE* 6.5 0.7 - - + -
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Residues in contact with VAL 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A PHE* 4.2 8.3 - - + -
183A LYS 3.8 0.7 - - - +
184A THR* 3.5 4.0 - - - -
185A LEU* 2.9 53.4 + - + +
187A GLU* 3.1 45.3 - - + +
197A LYS* 4.1 5.2 - - + +
198A PRO* 1.3 79.7 - - - +
200A THR* 1.3 61.6 + - - +
201A ILE* 4.0 9.3 + - + -
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Residues in contact with THR 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A SER* 3.8 24.9 - - - +
183A LYS 3.6 8.7 - - - +
184A THR* 3.1 17.7 + - - +
199A VAL* 1.3 71.2 - - - +
201A ILE* 1.3 70.0 + - - +
202A SER* 5.6 0.4 - - - +
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Residues in contact with ILE 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A VAL* 4.0 14.8 - - + -
152A PHE* 3.8 31.6 - - + -
181A LEU 3.5 1.7 - - - +
182A SER* 3.6 1.5 - - - -
183A LYS 2.9 31.4 + - - +
185A LEU* 4.3 9.4 - - + -
199A VAL* 4.4 13.9 - - + +
200A THR* 1.3 83.6 - - - +
202A SER* 1.3 72.3 + - - +
203A PHE* 3.7 29.8 - - + -
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Residues in contact with SER 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A TYR* 4.8 19.0 - - - -
181A LEU 3.2 8.2 + - - -
182A SER* 3.7 18.0 + - - -
200A THR* 5.6 0.5 - - - +
201A ILE* 1.3 80.2 - - - +
203A PHE* 1.3 63.3 + - - +
204A ALA 4.4 0.3 + - - -
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Residues in contact with PHE 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ILE* 4.8 5.8 - - + -
140A VAL* 3.7 40.8 - - + -
143A GLU* 4.3 20.4 - - + -
157A VAL* 3.8 29.4 - - + -
159A VAL* 4.1 18.1 - - + +
161A ARG* 4.4 3.6 - - - +
180A TYR* 3.6 4.6 - - - -
181A LEU* 3.0 33.1 + - + +
183A LYS* 4.0 23.8 - - + -
185A LEU* 5.2 3.1 - - + -
201A ILE* 3.7 43.1 - - + -
202A SER* 1.3 76.6 - - - +
204A ALA* 1.3 64.0 + - - +
205A ASN 3.5 0.3 + - - -
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Residues in contact with ALA 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A GLU* 5.4 0.8 + - - -
159A VAL* 3.8 8.7 - - - +
161A ARG* 2.8 39.0 + - - +
178A THR* 3.7 11.4 - - + -
179A SER 3.8 5.4 - - - -
180A TYR* 3.8 15.1 - - + -
202A SER 4.4 0.4 + - - -
203A PHE* 1.3 72.3 - - - +
205A ASN* 1.3 58.4 + - - +
206A HIS* 4.4 0.9 - - + -
1E NAG 3.5 35.2 - - - +
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Residues in contact with ASN 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A VAL* 4.1 1.7 - - + -
160A TYR* 3.1 27.8 + - - +
178A THR* 3.5 2.4 - - - +
179A SER* 2.8 35.3 + - - +
181A LEU* 3.9 29.8 - - + +
203A PHE 3.5 0.2 + - - -
204A ALA* 1.3 72.6 - - - +
206A HIS* 1.3 65.7 + - - +
207A THR* 3.4 1.8 + - - +
1F NAG 1.4 65.9 + - - +
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Residues in contact with HIS 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A PRO* 3.7 9.8 - - + +
160A TYR* 3.1 13.2 + - - +
161A ARG* 3.2 26.5 - - + -
162A CYS* 3.0 43.7 + - + +
175A ASN* 3.4 29.9 - - + +
177A SER 3.9 4.5 - - - -
178A THR* 3.8 9.0 - - + -
204A ALA* 4.4 0.4 - - + -
205A ASN* 1.3 71.8 - - - +
207A THR* 1.3 60.0 + - - +
208A SER 3.7 0.2 - - - -
209A CYS* 4.9 0.7 - - - -
1E NAG 2.9 40.1 + - - -
1F NAG 3.0 18.5 + - - +
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Residues in contact with THR 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A PRO* 4.0 6.5 - - - +
177A SER* 2.8 32.4 + - - -
178A THR* 4.1 2.1 + - - -
179A SER* 4.0 13.9 + - - -
205A ASN* 3.4 20.6 + - - +
206A HIS* 1.3 74.0 - - - +
208A SER* 1.3 64.1 + - - +
1F NAG 3.3 36.9 + - - +
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Residues in contact with SER 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A PRO* 4.2 4.2 - - - +
162A CYS* 3.6 0.7 - - - -
175A ASN* 3.3 7.3 - - - +
176A THR* 2.7 44.4 + - - -
177A SER* 2.7 25.0 + - - -
206A HIS 3.7 1.0 - - - -
207A THR* 1.3 83.3 + - - +
209A CYS* 1.3 67.2 + - - +
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Residues in contact with CYS 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A CYS* 3.5 23.6 - - - +
132A MET* 3.4 5.6 - - - -
133A PRO* 3.3 35.7 - - - +
162A CYS* 2.0 44.9 - - - -
174A MET 3.1 7.0 - - - +
176A THR* 4.2 3.6 - - - -
208A SER* 1.3 76.6 - - - +
210A ARG* 1.3 64.3 + - - +
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Residues in contact with ARG 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A CYS* 3.8 6.3 - - - -
174A MET 2.9 25.8 + - - +
176A THR* 3.8 32.3 + - + +
209A CYS* 1.3 76.8 - - - +
211A CYS* 1.3 75.2 + - - +
212A MET* 3.2 23.3 + - + +
237L SER* 4.9 11.7 + - - -
240L GLU* 5.0 4.8 + - - -
325L HIS* 4.4 21.1 - - - -
326L GLU 5.8 5.8 - - - -
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Residues in contact with CYS 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A CYS* 3.7 22.2 - - - +
165A CYS 4.6 0.9 - - - -
166A CYS* 2.0 54.7 - - + -
167A ASN 5.1 0.2 - - - -
171A LEU* 4.8 13.8 - - + +
172A GLN 3.7 4.7 - - - -
210A ARG* 1.3 79.8 - - - +
212A MET* 1.3 59.5 + - - +
194N TYR* 5.4 14.2 - - + +
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Residues in contact with MET 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A LEU* 4.1 4.5 - - - -
172A GLN* 2.7 37.2 + - - +
174A MET* 3.4 34.3 - - + +
175A ASN 5.1 2.5 - - - +
176A THR* 4.2 24.5 - - - -
210A ARG* 3.7 24.7 - - + +
211A CYS* 1.3 78.4 - - - +
213A SER* 1.3 64.2 + - - +
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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