Contacts of the strand formed by residues 200 - 206 (chain A) in PDB entry 6PB4
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 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A THR* 6.2 2.2 - - - -
28A LEU 3.2 18.2 - - - +
29A GLU* 3.9 15.5 + - + +
31A LEU* 4.8 2.0 - - - -
186A ASN 3.4 1.2 - - - +
187A VAL* 3.4 4.3 - - - +
188A GLU* 2.9 60.8 + - + +
189A ALA 3.3 20.5 + - - +
190A ALA* 3.1 16.8 - - + +
191A ARG* 4.4 5.1 - - - +
199A ASP* 1.3 75.8 - - - +
201A LEU* 1.3 57.9 + - - +
202A VAL* 4.8 11.2 - - + -
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Residues in contact with LEU 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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26A VAL 3.7 1.7 - - - +
28A LEU* 2.9 40.5 + - + +
31A LEU* 4.0 16.6 - - + +
36A GLY 3.1 24.9 - - - +
39A LEU* 3.9 9.4 - - + -
40A GLY* 3.2 28.5 - - - +
43A LEU* 4.0 5.4 - - + -
185A TYR* 3.4 28.9 - - + -
186A ASN 3.3 9.9 - - - +
187A VAL* 3.9 2.9 - - + -
200A LYS* 1.3 72.5 - - - +
202A VAL* 1.3 60.0 + - - +
203A ILE* 3.8 23.7 + - + +
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Residues in contact with VAL 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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17A GLU* 4.3 5.6 - - - +
25A LYS* 4.5 17.9 - - + -
26A VAL 3.3 16.2 - - - +
27A THR* 4.1 20.6 - - + +
28A LEU 4.7 0.7 - - - +
185A TYR* 3.2 2.8 - - - -
186A ASN* 2.9 43.7 + - + +
188A GLU* 3.6 23.3 - - - +
200A LYS* 4.8 12.6 - - + -
201A LEU* 1.3 75.1 - - - +
203A ILE* 1.3 63.6 + - - +
204A GLU* 3.9 3.0 + - + +
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Residues in contact with ILE 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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25A LYS* 3.3 3.2 - - - -
26A VAL* 2.9 42.6 + - + +
40A GLY* 4.8 2.0 - - - +
43A LEU* 3.3 37.9 - - + -
44A ARG* 6.3 0.2 - - + -
47A LEU* 4.6 7.2 - - + -
183A ILE* 4.2 17.5 - - + -
184A ALA 3.2 13.5 - - - +
185A TYR* 3.7 16.2 - - + -
201A LEU* 3.8 16.6 - - + +
202A VAL* 1.3 74.8 - - - +
204A GLU* 1.3 68.3 + - - +
205A MET* 5.0 8.6 - - + +
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Residues in contact with GLU 204 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A HIS* 4.4 4.7 + - - +
24A ALA 3.6 5.6 - - - +
25A LYS* 2.9 46.0 + - + +
182A ARG* 3.5 25.7 + - - +
183A ILE* 3.3 8.4 - - - +
184A ALA* 2.8 47.3 + - + +
186A ASN* 4.1 18.3 + - - +
202A VAL* 4.8 7.0 - - + +
203A ILE* 1.3 75.3 - - - +
205A MET* 1.3 59.9 + - - +
1090C ASN* 4.0 7.9 - - - +
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Residues in contact with MET 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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22A THR 4.1 1.8 - - - +
23A HIS* 3.0 11.7 - - - -
24A ALA* 2.9 40.0 + - + +
25A LYS* 5.7 0.2 - - - -
26A VAL* 6.5 0.9 - - + -
47A LEU* 3.8 40.6 - - + +
51A MET* 6.2 2.5 - - + -
180A VAL* 5.0 11.2 - - + -
182A ARG* 3.5 11.2 - - - +
183A ILE* 4.3 9.0 - - + -
203A ILE* 5.0 8.3 - - + +
204A GLU* 1.3 75.8 - - - +
206A GLU* 1.3 70.4 + - - +
207A THR* 4.9 13.7 - - + +
211A ILE* 5.9 4.9 - - - -
213A PRO* 5.5 13.5 - - - -
216A ALA* 5.8 7.2 - - + -
217A ILE* 6.2 3.1 - - + -
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Residues in contact with GLU 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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22A THR* 3.0 37.7 + - + +
23A HIS* 4.3 10.8 - - + +
180A VAL* 3.6 3.3 - - - +
181A GLU* 2.7 37.6 + - + +
182A ARG* 2.8 53.8 + - + +
205A MET* 1.3 77.0 - - - +
207A THR* 1.3 56.3 + - - +
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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