Contacts of the strand formed by residues 204 - 211 (chain A) in PDB entry 4CAA
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 HIS 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A GLN 3.5 13.8 + - - -
202A ASP* 2.8 37.5 + - - -
203A THR* 1.3 82.0 + - - +
205A GLN* 1.3 68.3 + - - +
206A SER* 3.2 7.6 + - - +
219A PRO* 4.1 3.8 - - - -
220A MET* 2.7 36.9 + - + +
222A SER* 5.3 0.2 + - - -
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Residues in contact with GLN 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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203A THR* 6.2 0.6 - - - +
204A HIS* 1.3 75.0 - - - +
206A SER* 1.3 59.5 + - - +
217A MET* 3.4 26.2 - - + +
218A VAL* 3.4 23.4 + - - -
219A PRO* 3.4 20.6 - - - +
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Residues in contact with SER 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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204A HIS* 3.2 3.4 + - - -
205A GLN* 1.3 74.7 - - - +
207A ARG* 1.3 64.7 + - - +
217A MET* 3.2 14.8 - - - +
218A VAL* 2.7 30.3 + - - +
220A MET* 2.8 40.5 - - - +
365B ARG* 6.0 3.6 - - - -
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Residues in contact with ARG 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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206A SER* 1.3 77.4 - - - +
208A PHE* 1.3 59.0 - - - +
209A TYR* 2.7 50.6 + - + -
215A TRP* 3.3 59.4 - - + +
216A VAL 3.3 5.2 - - - +
217A MET* 3.9 9.6 - - - -
220A MET* 3.9 6.7 - - - +
367B ASN* 3.5 23.5 + - - +
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Residues in contact with PHE 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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207A ARG* 1.3 73.4 - - - +
209A TYR* 1.3 79.0 + - - +
210A LEU* 3.4 11.8 + - + -
215A TRP* 3.3 1.8 - - - -
216A VAL* 2.8 32.7 + - + +
218A VAL* 3.8 25.6 - - + -
220A MET* 5.1 1.1 - - + -
289A PRO* 4.2 8.7 - - + -
366B PHE 4.1 1.8 - - - -
367B ASN* 3.6 12.6 - - - -
368B ARG 3.3 32.8 - - - -
369B PRO* 3.4 9.9 - - + -
370B PHE* 3.8 17.9 - + - -
388B VAL* 4.3 5.4 - - + -
389B THR 3.5 22.4 - - - -
391B PRO* 3.8 29.4 - - + -
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Residues in contact with TYR 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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207A ARG* 2.7 42.1 + - + -
208A PHE* 1.3 75.6 - - - +
210A LEU* 1.3 66.8 + - - +
211A SER* 3.2 21.3 + - - +
212A LYS* 4.0 10.5 - - - -
214A LYS 3.4 4.0 - - - -
215A TRP* 3.4 38.4 - + + -
257A GLN* 5.1 7.1 + - - +
367B ASN* 2.9 40.4 + - - +
368B ARG* 3.8 8.0 - - + +
369B PRO* 3.5 20.6 - - - +
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Residues in contact with LEU 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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208A PHE* 3.4 18.9 + - + +
209A TYR* 1.3 73.4 - - - +
211A SER* 1.3 61.4 + - - +
214A LYS* 2.8 42.1 + - + +
215A TRP* 5.0 1.3 - - - -
216A VAL* 4.7 13.7 - - + -
369B PRO* 4.4 11.8 - - - +
389B THR 3.6 16.5 - - - +
390B ASN* 3.0 42.6 - - + +
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Residues in contact with SER 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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209A TYR* 3.0 13.3 - - - +
210A LEU* 1.3 77.6 - - - +
212A LYS* 1.3 67.3 + - - +
213A LYS 4.0 1.9 + - - -
214A LYS* 2.8 57.2 + - - +
257A GLN* 4.9 9.6 - - - +
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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