Contacts of the strand formed by residues 190 - 198 (chain A) in PDB entry 4U7B
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 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A TRP* 3.3 47.3 - - + -
160A ILE 3.7 12.1 - - - +
161A PHE* 4.2 26.2 - - + +
162A PHE* 3.9 3.1 - - - -
186A ARG 3.8 18.9 + - - -
187A PHE* 5.3 6.0 - - - +
188A GLY 3.8 15.3 - - - +
189A LYS* 1.3 76.1 - - - +
191A THR* 1.3 61.8 + - - +
210A PRO* 3.4 22.0 - - - +
211A GLY* 3.7 8.0 + - - +
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Residues in contact with THR 191 (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 TRP* 3.9 2.9 - - - -
160A ILE* 3.0 36.4 + - - +
162A PHE* 3.7 18.9 - - + -
190A LYS* 1.3 74.8 - - - +
192A MET* 1.3 63.0 + - - +
193A LEU 3.6 0.9 + - - -
207A LEU* 4.0 11.5 - - + +
208A LEU 3.2 21.1 - - - +
209A LYS 4.6 1.1 - - - -
210A PRO* 3.8 20.6 - - + -
303A TYR* 3.8 19.1 - - + -
306A VAL* 4.1 17.5 - - - +
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Residues in contact with MET 192 (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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157A GLU* 3.7 37.2 - - + -
158A LYS* 3.9 9.0 - - - +
159A TRP* 3.6 46.3 - - + +
191A THR* 1.3 73.9 - - - +
193A LEU* 1.3 60.6 + - - +
194A CYS* 4.1 3.6 - - - -
207A LEU* 3.4 4.0 - - - +
208A LEU* 3.0 48.9 + - + +
209A LYS 4.9 1.0 + - - -
212A GLU 4.4 2.7 + - - +
213A THR* 5.0 4.3 - - - +
214A VAL* 4.1 30.7 - - + +
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Residues in contact with LEU 193 (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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157A GLU* 3.1 6.1 - - - +
158A LYS* 2.9 39.3 + - + +
160A ILE* 3.9 12.8 - - + -
191A THR 3.6 0.2 + - - -
192A MET* 1.3 73.8 - - - +
194A CYS* 1.3 74.7 + - - +
195A VAL* 4.2 23.0 + - + -
205A TYR* 3.6 32.8 - - + -
206A GLU 3.8 4.5 - - - +
207A LEU* 3.9 15.3 - - + -
288A PHE* 4.4 7.5 - - + -
291A MET* 4.1 15.0 - - + -
310A LEU* 3.8 26.9 - - + -
314A PHE* 4.7 4.3 - - + -
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Residues in contact with CYS 194 (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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156A ASP 3.8 3.8 - - - -
157A GLU* 3.5 31.9 - - - +
192A MET* 4.1 6.5 - - - -
193A LEU* 1.3 72.5 - - - +
195A VAL* 1.3 60.5 - - - +
196A TRP* 3.8 23.6 - - + -
205A TYR* 3.1 4.5 - - - +
206A GLU 2.9 42.2 + - - +
208A LEU* 4.5 7.4 - - - -
214A VAL* 3.6 22.4 - - - -
222A GLN* 4.1 13.7 - - - +
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Residues in contact with VAL 195 (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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155A GLY* 3.2 18.9 - - - -
156A ASP 3.2 10.2 + - - +
193A LEU* 4.2 14.1 - - + -
194A CYS* 1.3 75.8 - - - +
196A TRP* 1.3 78.7 + - - +
197A TRP* 4.3 9.7 - - + +
202A VAL* 3.9 14.6 - - + -
204A TYR 3.8 3.1 - - - -
205A TYR* 3.8 17.3 - - + -
283A SER* 4.8 0.4 + - - -
287A LEU* 4.5 13.5 - - + -
288A PHE* 3.9 32.3 - - + -
314A PHE* 4.3 11.7 - - + -
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Residues in contact with TRP 196 (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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153A VAL* 4.7 3.8 - - + -
154A THR 3.2 11.0 - - - +
155A GLY* 3.4 26.8 - - - -
156A ASP 5.3 2.2 - - - -
157A GLU* 5.2 2.5 - - - -
194A CYS* 3.8 31.0 - - + -
195A VAL* 1.3 81.1 - - - +
197A TRP* 1.3 62.8 + - - +
203A ILE* 3.1 20.0 + - - -
204A TYR* 3.1 49.3 + + + +
205A TYR* 4.6 0.2 - - - -
206A GLU* 4.8 1.3 - - + -
219A TYR* 3.8 30.5 + + - -
222A GLN* 3.6 33.9 - - + -
223A LEU* 5.7 2.2 - - + -
226A LEU* 4.0 29.1 - - + +
246A PHE* 3.8 32.9 - + - -
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Residues in contact with TRP 197 (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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153A VAL* 3.4 4.0 - - - +
154A THR* 3.1 36.3 + - + +
195A VAL* 4.3 7.0 - - + -
196A TRP* 1.3 82.4 - - - +
198A ASP* 1.3 82.9 + - - +
201A GLY 3.7 1.1 - - - +
202A VAL* 3.6 21.3 - - + +
203A ILE* 3.6 13.6 - - - +
282A PRO* 3.6 23.8 - - + -
283A SER* 3.3 40.6 + - - +
286A HIS* 4.4 15.5 - + - -
287A LEU* 3.1 36.1 - - + +
322A TYR* 3.5 34.3 - + + -
325A GLY 4.6 0.2 - - - -
326A ILE* 3.5 20.6 - - + -
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Residues in contact with ASP 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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150A HIS 5.2 3.3 - - - +
152A ILE 3.2 25.1 - - - +
153A VAL* 4.1 6.4 - - + +
197A TRP* 1.3 84.3 - - - +
199A GLN* 1.3 58.2 + - + +
200A SER* 3.0 13.2 + - - -
201A GLY* 2.6 30.6 + - - +
203A ILE* 3.6 9.6 - - - +
234A ARG* 3.1 39.6 + - - +
237A TYR* 4.8 10.0 + - - -
322A TYR* 3.6 7.1 - - - +
326A ILE* 4.1 5.4 - - - -
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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