Contacts of the strand formed by residues 196 - 209 (chain B) in PDB entry 4KGG
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 ASN 196 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151B GLY 3.5 8.8 + - - -
152B VAL* 4.7 5.7 - - - +
195B SER* 1.3 76.9 + - - +
197B TRP* 1.3 62.5 + - - +
198B PHE* 4.0 26.3 - - - -
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Residues in contact with TRP 197 (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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149B LEU* 3.9 10.3 - - + -
150B GLY* 3.0 52.1 - - - -
151B GLY* 3.0 41.5 + - - +
152B VAL 4.0 1.6 - - - -
153B GLY 3.5 26.3 + - - -
162B ILE* 4.3 13.5 - - + -
186B PRO* 3.8 45.3 - - + +
187B CYS* 3.9 22.1 - - + +
195B SER 4.3 1.3 - - - -
196B ASN* 1.3 79.1 + - - +
198B PHE* 1.3 78.9 + - - +
199B ASP 4.3 2.0 - - - -
224B LEU* 4.3 15.9 - - + -
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Residues in contact with PHE 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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148B GLN* 4.0 17.9 - - + +
149B LEU 3.3 14.6 - - - -
150B GLY* 4.3 1.3 - - - -
186B PRO 5.7 0.2 - - - +
196B ASN* 4.0 22.2 - - + -
197B TRP* 1.3 86.0 - - - +
199B ASP* 1.3 64.3 + - - +
226B ARG* 4.5 20.4 - - + -
232B ARG* 5.6 8.5 - - - -
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Residues in contact with ASP 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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148B GLN* 3.1 6.1 + - - +
149B LEU* 2.7 47.8 + - + +
184B GLN* 3.1 27.5 - - - +
186B PRO* 3.8 33.0 - - + +
197B TRP* 4.1 2.2 - - + -
198B PHE* 1.3 76.9 - - - +
200B SER* 1.3 68.3 + - - +
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Residues in contact with SER 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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146B LYS* 2.7 43.4 + - - +
147B VAL 3.5 5.4 + - - -
148B GLN* 4.2 7.6 - - - +
149B LEU* 5.5 0.7 - - - -
184B GLN* 4.4 3.6 + - - +
199B ASP* 1.3 91.9 + - - +
201B SER* 1.3 60.2 + - - +
202B PHE 4.3 0.7 + - - -
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Residues in contact with SER 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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146B LYS* 3.1 7.6 - - - +
147B VAL* 3.0 40.1 + - - -
149B LEU* 4.8 5.2 - - - -
164B HIS* 2.8 36.0 + - - +
182B SER* 4.1 9.7 + - - -
184B GLN* 3.4 29.0 + - - +
199B ASP 4.4 0.2 + - - -
200B SER* 1.3 73.9 + - - +
202B PHE* 1.3 62.1 + - - +
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Residues in contact with PHE 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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142B TYR* 4.1 14.6 - + - -
144B TYR* 3.9 18.8 - + + -
145B SER 3.5 7.2 - - - -
146B LYS* 3.7 25.8 - - + -
182B SER* 4.7 3.1 + - - -
184B GLN* 5.2 0.4 - - - +
200B SER 4.2 1.0 - - - -
201B SER* 1.3 76.6 + - - +
203B LEU* 1.3 84.7 + - - +
204B GLY 3.9 3.6 - - - -
234B TYR* 4.0 22.9 - + - -
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Residues in contact with LEU 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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144B TYR* 3.1 5.2 - - - +
145B SER 2.9 29.8 + - - +
164B HIS* 3.5 47.3 - - + +
165B GLY* 3.8 9.0 - - - -
166B LEU* 3.9 18.2 - - + -
180B LEU* 3.8 18.6 - - + +
181B VAL 4.0 21.1 - - - +
182B SER* 3.5 23.3 - - - +
201B SER* 4.8 0.2 - - - +
202B PHE* 1.3 84.3 - - - +
204B GLY* 1.3 58.8 + - - +
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Residues in contact with GLY 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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142B TYR* 3.7 23.1 - - - -
143B ILE 3.2 11.4 - - - -
144B TYR* 4.1 1.8 - - - -
180B LEU* 3.8 11.9 - - - +
202B PHE* 3.9 4.7 - - - -
203B LEU* 1.3 75.9 - - - +
205B GLY* 1.3 57.3 + - - -
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Residues in contact with GLY 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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142B TYR* 3.5 13.7 - - - -
143B ILE* 2.8 38.4 + - - +
180B LEU* 3.6 18.9 - - - +
204B GLY* 1.3 75.0 - - - -
206B VAL* 1.3 58.0 + - - -
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Residues in contact with VAL 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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140B TYR* 4.0 32.0 - - + -
141B TYR 3.2 13.9 - - - +
142B TYR* 4.0 18.6 - - + +
180B LEU* 5.9 0.5 - - - +
205B GLY* 1.3 72.3 - - - -
207B VAL* 1.3 67.8 + - - +
240B VAL* 4.1 14.4 - - + -
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Residues in contact with VAL 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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140B TYR* 4.3 5.6 - - - -
141B TYR* 3.0 34.4 + - - +
143B ILE* 3.8 31.9 - - + -
179B LEU* 4.3 27.8 - - + +
180B LEU* 5.1 8.3 - - + -
205B GLY 3.9 2.7 + - - +
206B VAL* 1.3 77.1 - - - +
208B HIS* 1.3 62.6 + - - +
209B LEU* 3.7 26.8 + - + -
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Residues in contact with HIS 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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138B ALA* 4.9 3.3 - - + +
139B GLY* 3.5 33.7 + - - -
140B TYR* 3.8 38.5 - + + -
168B LYS* 4.7 5.7 + - - +
207B VAL* 1.3 73.9 - - - +
209B LEU* 1.3 75.3 + - - +
210B GLU* 3.4 28.5 + - - +
213B GLU* 4.0 5.7 - - - +
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Residues in contact with LEU 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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135B VAL* 3.8 31.2 - - + -
137B LYS 4.5 0.7 - - - +
138B ALA* 3.3 3.6 - - - +
139B GLY 3.0 34.2 + - - +
141B TYR* 3.8 23.8 - - + -
143B ILE* 4.7 3.4 - - + -
168B LYS* 3.7 27.1 - - + -
179B LEU* 5.1 0.9 - - + -
207B VAL* 3.9 23.6 - - + +
208B HIS* 1.3 87.3 + - - +
210B GLU* 1.3 62.9 + - - +
213B GLU* 3.7 6.5 - - + +
215B VAL* 3.9 26.7 - - + -
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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