Contacts of the strand formed by residues 203 - 211 (chain A) in PDB entry 4FYT
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 VAL 203 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A MET* 3.4 5.4 - - - -
200A GLU 2.9 37.7 + - - +
201A GLY 3.4 0.2 - - - -
202A ASN* 1.3 84.2 - - + +
204A ARG* 1.3 68.6 + - - +
205A LYS* 3.5 29.4 + - + +
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Residues in contact with ARG 204 (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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101A TYR* 5.3 4.0 - - - +
197A GLU* 3.2 43.6 + - - +
198A TYR* 3.7 11.3 + - - +
199A MET* 3.5 38.5 - - + +
202A ASN 3.8 3.6 + - - -
203A VAL* 1.3 78.1 - - - +
205A LYS* 1.3 71.3 + - - +
206A VAL* 3.8 16.0 + - + +
1024A SO4 4.9 2.4 + - - -
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Residues in contact with LYS 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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196A SER 3.9 0.2 - - - +
197A GLU* 3.3 6.2 - - - +
198A TYR* 2.8 80.6 + - + +
200A GLU* 3.5 25.6 + - + -
203A VAL* 3.5 28.4 + - + +
204A ARG* 1.3 78.3 - - - +
206A VAL* 1.3 62.2 + - - +
207A VAL 4.2 0.2 - - - -
286A GLU* 3.0 41.5 + - + +
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Residues in contact with VAL 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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93A LEU* 3.9 56.1 - - + +
101A TYR* 4.2 15.9 - - + +
195A ARG* 4.1 27.6 - - + -
196A SER 3.5 8.1 - - - +
197A GLU* 4.1 6.3 - - + -
204A ARG* 3.8 25.3 + - + +
205A LYS* 1.3 78.3 - - - +
207A VAL* 1.3 65.2 + - - +
243A LEU* 5.1 3.6 - - - +
284A VAL 4.5 1.0 - - - +
285A SER* 5.3 1.7 - - - -
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Residues in contact with VAL 207 (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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93A LEU* 4.1 2.7 - - - -
195A ARG* 3.2 8.0 - - - +
196A SER* 2.8 43.6 + - - +
198A TYR* 3.8 30.1 - - + +
205A LYS* 5.6 0.2 - - + -
206A VAL* 1.3 78.3 - - - +
208A ALA* 1.3 71.1 + - - +
209A THR* 4.1 2.2 - - - -
283A ILE* 4.2 3.4 - - + -
284A VAL 3.5 12.3 - - - +
285A SER* 4.1 15.7 - - - -
286A GLU 5.6 0.7 - - - +
287A PHE* 4.0 15.0 - - + -
346A LEU* 4.1 23.1 - - + -
347A PRO* 5.4 0.7 - - + -
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Residues in contact with ALA 208 (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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91A PRO* 3.7 31.0 - - + -
93A LEU* 3.9 10.5 - - + +
186A LEU* 4.1 6.3 - - + -
193A PHE* 3.7 20.9 - - + -
194A TYR 3.5 4.7 - - - -
207A VAL* 1.3 71.7 - - - +
209A THR* 1.3 62.5 - - - +
283A ILE* 3.2 4.3 - - - +
284A VAL* 2.8 39.0 + - + +
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Residues in contact with THR 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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193A PHE* 3.4 4.8 - - - -
194A TYR* 2.8 70.8 + - + +
196A SER* 4.3 10.3 - - - -
207A VAL* 4.1 2.0 - - - -
208A ALA* 1.3 78.2 - - - +
210A THR* 1.3 72.1 + - - +
282A PHE 3.5 6.3 - - - -
283A ILE* 3.5 18.9 - - - +
346A LEU* 3.5 34.0 - - + +
349A PHE* 5.9 0.3 - - - -
361A THR* 4.8 0.9 - - - +
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Residues in contact with THR 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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192A GLY 3.0 7.6 - - - +
193A PHE* 3.6 15.7 - - + -
194A TYR* 3.7 7.3 - - - -
209A THR* 1.3 87.2 + - - +
211A GLN* 1.3 65.9 + - - +
212A MET* 3.6 29.6 - - + -
280A LEU 4.0 1.8 + - - -
281A ALA* 3.2 15.2 - - - +
282A PHE* 3.1 40.6 + - + +
283A ILE* 4.6 1.9 - - - +
349A PHE* 4.5 8.8 - - - -
356A ASN* 5.1 2.8 + - - -
361A THR* 4.6 8.3 + - - +
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Residues in contact with GLN 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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190A LEU 3.6 23.1 - - - +
191A ALA* 3.8 2.0 - - + -
192A GLY* 2.8 34.2 + - - -
194A TYR* 3.8 5.5 - - + +
210A THR* 1.3 74.7 - - - +
212A MET* 1.3 60.2 + - - +
213A GLN* 3.1 46.3 + - - +
216A ASP* 3.6 5.4 - - - +
349A PHE* 3.6 18.3 - - + -
350A ASN* 5.4 8.7 - - + +
351A ALA* 5.6 2.5 - - - +
354A MET* 3.4 35.1 - - - +
356A ASN* 5.7 1.8 - - - -
361A THR* 4.5 0.2 + - - -
896A PHE* 5.3 4.7 - - + -
1B L2O 3.6 12.4 - - + +
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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