Contacts of the strand formed by residues 206 - 210 (chain A) in PDB entry 6HBU
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 ILE 206 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ALA* 3.7 18.8 - - + -
37A LEU* 4.1 7.2 - - + -
108A ILE* 3.7 32.3 - - + -
117A PHE* 3.9 15.7 - - + -
120A ASN 4.2 3.9 + - - +
121A SER* 3.3 14.0 - - - -
122A GLY 3.1 21.5 + - - -
204A PRO* 3.7 2.8 - - - +
205A SER* 1.3 75.5 - - - +
207A LEU* 1.3 63.6 + - - +
208A PHE* 3.6 30.5 - - + -
237A THR* 3.5 18.4 - - + -
239A ILE* 3.8 15.0 - - + -
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Residues in contact with LEU 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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122A GLY 3.5 5.8 - - - +
124A VAL* 6.0 2.7 - - + -
199A GLU 3.8 12.8 - - - +
200A LEU* 5.1 5.8 - - + -
204A PRO* 3.7 36.3 - - + +
205A SER 5.0 0.2 - - - +
206A ILE* 1.3 78.7 - - - +
208A PHE* 1.3 63.5 + - - +
209A LEU* 3.6 32.5 - - + -
228A LEU* 4.1 13.0 - - + -
231A MET* 4.2 19.1 - - - -
236A ARG* 5.7 1.3 - - + -
237A THR 3.0 11.5 + - - +
238A ILE* 3.3 22.7 - - + +
239A ILE 3.0 24.5 + - - +
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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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37A LEU* 3.6 18.4 - - + -
90A LEU* 3.8 17.3 - - + -
93A LEU* 3.5 37.7 - - + -
94A ALA* 3.8 21.3 - - + -
117A PHE* 4.2 11.7 - + - -
121A SER* 4.6 5.2 - - - -
122A GLY 2.6 21.2 + - - +
123A TYR* 3.4 21.3 - - + -
124A VAL* 2.8 25.4 + - - +
206A ILE* 3.6 19.3 - - + -
207A LEU* 1.3 75.6 - - - +
209A LEU* 1.3 65.1 + - - +
239A ILE* 3.2 34.5 - - + -
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Residues in contact with LEU 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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90A LEU* 3.3 6.2 - - - +
123A TYR* 5.3 0.4 - - - -
124A VAL* 3.8 23.1 - - + -
196A ILE* 4.4 16.6 - - + -
200A LEU* 6.1 0.4 - - + -
207A LEU* 3.6 28.7 - - + +
208A PHE* 1.3 77.3 - - - +
210A ASP* 1.3 61.1 + - - +
211A GLN 3.6 1.5 + - - -
212A PRO* 3.6 30.5 - - + -
224A VAL* 5.7 0.2 - - + -
228A LEU* 4.1 19.7 - - + -
238A ILE* 3.7 19.3 - - + -
239A ILE 3.0 7.7 + - - -
240A PHE* 3.2 33.5 - - + +
241A SER 3.3 6.9 + - - -
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Residues in contact with ASP 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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87A SER* 2.8 34.2 + - - -
90A LEU* 3.8 7.5 - - + +
123A TYR* 3.2 24.9 + - + +
124A VAL* 2.9 21.6 + - - +
125A VAL 4.0 0.5 - - - +
126A GLN* 3.6 29.9 + - - +
192A LYS* 3.4 14.0 + - - -
209A LEU* 1.3 70.6 - - - +
211A GLN* 1.3 70.8 + - - +
212A PRO* 4.5 0.4 - - - +
241A SER* 3.1 16.3 + - - -
1502A MG 3.2 4.0 - - - -
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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