Contacts of the strand formed by residues 194 - 201 (chain A) in PDB entry 4DNL
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 PRO 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A LEU* 3.8 19.5 - - + -
192A SER* 3.4 9.4 - - - +
193A ASP* 1.3 90.3 - - - +
195A TYR* 1.3 58.3 + - - +
214A THR* 3.5 0.7 - - - -
215A ILE* 3.0 38.5 + - - +
218A THR* 3.6 17.3 - - + +
221A PRO* 3.7 24.0 - - + -
223A TRP* 3.5 18.9 + - + -
244A ILE* 4.0 6.3 - - + -
245A TRP 3.2 10.8 - - - +
256A MSE 4.0 4.7 - - - -
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Residues in contact with TYR 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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194A PRO* 1.3 73.2 - - - +
196A VAL* 1.3 72.8 + - - +
197A LYS* 3.7 33.4 + - + -
211A LYS* 4.2 27.4 - - + -
212A THR* 3.4 11.4 - - - +
213A LYS 3.5 14.8 - - - +
214A THR* 3.7 20.6 - - - +
223A TRP* 3.9 2.7 - - - -
244A ILE* 3.4 4.3 - - - +
245A TRP* 2.9 59.2 + + + +
247A TRP* 3.7 21.5 - + + -
253A ASN* 2.8 34.2 + - - +
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Residues in contact with VAL 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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162A ILE* 4.4 2.7 - - + -
177A VAL* 3.8 17.9 - - + -
195A TYR* 1.3 78.0 - - - +
197A LYS* 1.3 65.1 + - - +
198A LEU* 4.1 11.1 + - + +
211A LYS* 3.0 7.1 - - - +
212A THR* 2.8 41.4 + - + +
223A TRP* 3.4 39.5 - - + -
242A VAL* 3.7 28.9 - - + -
243A GLU 3.3 10.1 - - - +
244A ILE* 4.1 9.2 - - + -
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Residues in contact with LYS 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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195A TYR* 3.7 33.8 + - + -
196A VAL* 1.3 72.3 - - - +
198A LEU* 1.3 65.9 + - - +
199A LYS* 5.4 15.3 - - + +
209A LYS* 5.0 11.2 - - + -
210A GLN 3.5 9.2 - - - +
211A LYS* 4.3 7.4 - - + -
241A SER 3.6 1.2 - - - +
242A VAL* 3.5 4.2 - - - -
243A GLU* 2.8 48.2 + - + +
245A TRP* 3.7 36.4 - - + +
253A ASN* 6.1 0.2 - - - +
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Residues in contact with LEU 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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175A VAL* 4.1 20.2 - - + -
177A VAL* 4.3 9.0 - - + -
196A VAL* 4.1 9.9 - - + +
197A LYS* 1.3 75.5 - - - +
199A LYS* 1.3 59.5 + - - +
208A SER 3.7 1.9 - - - +
209A LYS* 3.4 4.3 - - - +
210A GLN* 2.8 39.0 + - + +
227A PHE* 3.3 50.0 - - + -
229A PHE* 3.8 18.8 - - + -
240A LEU* 4.5 3.1 - - + -
241A SER 3.3 2.5 - - - +
242A VAL* 3.7 39.9 - - + -
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Residues in contact with LYS 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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197A LYS* 5.4 15.3 - - + +
198A LEU* 1.3 74.4 - - - +
200A LEU* 1.3 60.7 + - - +
201A ILE* 4.0 22.2 - - + -
203A ASP* 3.9 13.7 - - + +
206A ASN* 3.0 31.1 + - - +
208A SER* 3.5 18.4 - - - +
209A LYS* 4.3 17.4 - - + +
229A PHE* 4.3 1.5 - - - -
239A ARG 3.6 0.2 - - - +
240A LEU* 3.5 7.1 - - - +
241A SER* 2.8 41.6 + - - +
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Residues in contact with LEU 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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173A LEU* 3.7 26.0 - - + -
199A LYS* 1.3 71.4 - - - +
201A ILE* 1.3 60.3 + - - +
202A PRO 3.5 5.0 - - - +
203A ASP* 3.2 22.3 - - - +
208A SER* 2.8 19.6 + - - +
229A PHE* 3.7 38.6 - - + -
230A LYS 5.0 3.1 - - - +
231A LEU* 3.8 17.5 - - + -
235A ASP* 4.3 11.7 - - - +
238A ARG* 4.2 13.8 - - + -
239A ARG 3.3 11.4 - - - +
240A LEU* 3.9 11.2 - - + -
263A VAL* 3.9 13.5 - - + -
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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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199A LYS* 4.0 30.1 - - + -
200A LEU* 1.3 76.5 - - - +
202A PRO* 1.3 70.4 - - + +
203A ASP* 4.6 3.8 - - + +
238A ARG* 3.2 6.6 - - - +
239A ARG* 2.8 54.2 + - + +
241A SER* 4.0 20.9 - - - -
260A SER* 5.4 0.4 - - - -
284A GLU* 4.0 42.0 - - + +
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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