Contacts of the strand formed by residues 198 - 206 (chain N) in PDB entry 5U0A
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 THR 198 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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336C ARG* 3.5 21.4 + - - +
337C ASP* 4.2 16.4 + - - +
394C THR* 5.5 6.7 + - - -
29N TYR* 3.9 9.0 - - - +
196N THR* 3.6 3.7 + - - -
197N LEU* 1.3 82.2 - - - +
199N VAL* 1.3 68.7 + - - +
200N LEU* 3.5 23.8 - - + -
217N ARG 3.6 1.0 - - - +
218N GLN* 3.4 3.8 - - - +
219N ILE* 2.9 50.3 + - + +
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Residues in contact with VAL 199 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ARG* 6.5 0.2 - - - -
336C ARG* 4.1 4.0 + - - -
392C THR* 5.1 6.7 + - - +
394C THR* 4.2 28.5 + - + +
196N THR* 6.0 0.2 - - - +
198N THR* 1.3 83.5 + - - +
200N LEU* 1.3 63.1 + - - +
216N THR* 3.3 35.4 - - + +
217N ARG 3.7 4.7 - - - +
218N GLN* 4.2 26.9 - - + +
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Residues in contact with LEU 200 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C ARG* 2.4 37.5 - - - +
17N GLU* 3.6 7.4 - - - +
27N LEU* 3.3 25.1 - - + -
29N TYR* 4.8 4.5 - - + -
198N THR* 3.5 22.0 - - + -
199N VAL* 1.3 74.2 - - - +
201N ASN* 1.3 60.5 + - - +
202N ASP* 3.0 26.4 + - - +
216N THR* 3.7 7.0 - - - -
217N ARG* 3.0 59.7 + - - +
219N ILE* 4.8 3.1 - - + -
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Residues in contact with ASN 201 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C GLU* 3.4 10.7 + - - -
60C PRO* 5.0 16.4 - - - +
3K G 3.2 34.4 + - - +
17N GLU* 3.3 16.3 + - - +
18N HIS* 5.7 1.4 - - - +
200N LEU* 1.3 68.6 - - - +
202N ASP* 1.3 67.4 + - - +
214N TYR* 3.8 21.9 + - + +
215N SER* 3.4 10.2 - - - +
216N THR* 3.1 29.8 - - - +
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Residues in contact with ASP 202 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K G 4.2 1.7 + - - -
17N GLU* 4.0 8.3 - - - +
31N SER* 3.4 15.6 - - - -
32N ARG* 3.1 20.7 + - + -
33N SER* 3.0 25.0 - - - +
200N LEU* 3.0 19.5 + - - +
201N ASN* 1.3 83.4 - - - +
203N VAL* 1.3 67.0 + - - +
204N PRO* 2.9 5.1 - - - +
214N TYR* 3.1 4.8 - - - -
215N SER 2.9 8.3 + - - -
217N ARG* 2.8 49.3 + - + +
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Residues in contact with VAL 203 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32N ARG* 4.3 20.8 - - - +
36N ILE* 5.9 0.2 - - + -
55N LYS* 5.1 20.9 - - + +
202N ASP* 1.3 71.0 - - - +
204N PRO* 1.3 76.7 - - + +
205N LEU* 3.3 9.6 + - + +
214N TYR* 3.4 1.7 - - - -
215N SER* 2.9 50.4 + - - +
216N THR 4.2 8.7 - - - +
217N ARG* 5.0 4.8 - - + +
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Residues in contact with PRO 204 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32N ARG* 4.7 0.4 - - + -
33N SER* 4.3 6.1 - - - +
36N ILE* 3.8 44.6 - - + -
51N LEU* 3.3 30.8 - - + +
202N ASP 2.9 5.4 - - - +
203N VAL* 1.3 87.9 - - + +
205N LEU* 1.3 65.6 + - - +
206N SER 3.3 1.1 - - - +
207N PHE* 3.8 12.8 - - + -
213N ARG 4.0 0.2 - - - +
214N TYR* 3.3 28.0 - - + -
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Residues in contact with LEU 205 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50N PRO* 5.9 0.9 - - - +
51N LEU* 4.4 9.2 + - - +
203N VAL* 3.4 20.6 - - + +
204N PRO* 1.3 73.1 - - - +
206N SER* 1.3 63.3 + - - +
213N ARG* 3.0 47.5 + - + +
214N TYR 3.6 10.5 - - - +
215N SER* 3.4 30.1 - - - +
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Residues in contact with SER 206 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48N GLY* 4.3 10.7 + - - -
49N ASP 5.2 2.4 + - - -
51N LEU* 4.0 9.6 - - - -
204N PRO 3.3 1.2 - - - -
205N LEU* 1.3 82.7 - - - +
207N PHE* 1.3 63.5 + - - +
208N ASP* 3.4 20.9 + - - +
211N SER 4.4 10.3 - - - -
212N ARG* 3.4 21.0 - - - +
213N ARG* 3.5 16.9 + - - +
214N TYR* 4.9 1.9 - - - -
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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