Contacts of the strand formed by residues 208 - 214 (chain A) in PDB entry 3NFP
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 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A GLY* 4.7 3.0 - - - -
122A PRO* 4.4 23.5 - - + +
201A VAL 4.1 0.3 - - - +
202A ASN* 2.9 20.9 + - - +
203A HIS* 3.1 16.3 + - - -
206A SER* 2.6 32.1 + - - -
207A ASN* 1.3 75.6 - - - +
209A LYS* 1.3 66.2 + - - +
210A VAL* 4.1 10.8 - - + +
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Residues in contact with LYS 209 (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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201A VAL 3.8 4.9 - - - +
202A ASN* 3.4 35.2 - - + +
207A ASN* 3.1 29.7 + - - +
208A THR* 1.3 72.3 - - - +
210A VAL* 1.3 60.8 + - - +
211A ASP* 4.3 7.2 - - - +
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Residues in contact with VAL 210 (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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122A PRO* 5.7 7.4 - - + +
124A VAL* 3.9 30.9 - - + +
199A CYS 4.1 0.2 - - - +
201A VAL* 3.1 35.4 + - + +
208A THR* 4.1 10.5 - - + -
209A LYS* 1.3 74.1 - - - +
211A ASP* 1.3 71.8 + - - +
212A LYS* 4.2 6.6 + - + +
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Residues in contact with ASP 211 (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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198A ILE* 3.8 11.1 - - + +
199A CYS 3.1 7.0 - - - +
200A ASN* 3.3 31.8 - - - +
201A VAL 5.4 0.2 - - - +
209A LYS* 4.3 5.9 - - - +
210A VAL* 1.3 88.0 + - - +
212A LYS* 1.3 61.2 + - - +
213A LYS 4.0 1.0 + - - -
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Residues in contact with LYS 212 (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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124A VAL* 4.0 35.6 - - + +
126A PRO* 4.3 33.6 - - + +
143A CYS* 4.4 2.2 - - - -
198A ILE* 3.3 4.1 - - - +
199A CYS* 2.9 38.6 + - - -
210A VAL* 4.2 7.2 + - + +
211A ASP* 1.3 72.7 - - - +
213A LYS* 1.3 82.7 + - - +
214A VAL* 4.0 2.9 + - + +
122B GLU* 6.0 7.4 - - - -
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Residues in contact with LYS 213 (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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126A PRO* 4.9 3.1 - - - +
196A THR* 5.2 8.7 - - + -
197A TYR 3.6 5.6 - - - +
198A ILE* 4.1 19.1 - - + +
211A ASP 4.0 1.8 + - - -
212A LYS* 1.3 96.2 + - - +
214A VAL* 1.3 62.1 + - - +
215A GLU* 4.4 15.5 + - + +
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Residues in contact with VAL 214 (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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126A PRO* 4.1 25.1 - - + -
127A LEU 4.1 22.0 - - - +
128A ALA* 4.5 3.4 - - + -
141A LEU* 4.5 23.4 - - + +
142A GLY 4.3 10.3 - - - +
143A CYS* 4.4 16.4 - - - -
157A TRP* 4.5 12.3 - - + -
195A GLN 5.7 0.3 - - - +
196A THR* 5.5 2.3 - - - +
197A TYR* 2.9 31.6 + - + +
212A LYS* 4.4 2.7 - - + +
213A LYS* 1.3 78.8 - - - +
215A GLU* 1.3 72.5 + - - +
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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