Contacts of the helix formed by residues 202 - 211 (chain A) in PDB entry 5FHT
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 SER 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A LEU* 4.0 14.1 - - - +
113A GLY 2.8 23.7 + - - -
115A SER* 3.3 13.7 + - - -
184A VAL* 3.3 24.9 + - - -
185A ILE* 2.9 16.9 + - - -
186A GLY* 4.3 1.1 - - - +
200A ILE 3.6 1.3 + - - -
201A PRO* 1.3 72.7 - - - +
203A ASP* 1.3 60.4 + - - +
205A LEU* 3.2 11.5 + - - +
206A ARG* 2.8 31.1 + - - +
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Residues in contact with ASP 203 (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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113A GLY 3.7 0.7 - - - +
114A ARG* 3.4 14.6 + - - +
115A SER* 2.9 36.9 + - - +
116A ALA* 3.1 32.4 + - - +
201A PRO* 5.4 0.4 - - + -
202A SER* 1.3 76.5 - - - +
204A ARG* 1.3 62.1 + - - +
206A ARG* 2.9 27.9 + - - +
207A GLU* 3.3 28.2 + - - +
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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
----------------------------------------------------------
91A ASP* 4.9 3.9 + - - +
93A LYS* 4.1 8.3 - - - +
94A ALA* 3.7 28.7 - - + +
96A ILE* 4.7 2.9 - - + -
154A LEU 4.5 1.8 + - - -
155A PRO* 3.0 34.7 + - - +
157A THR* 3.0 32.7 + - - -
158A ASN 3.3 15.6 + - - -
159A VAL* 3.8 15.0 - - - +
200A ILE* 4.2 11.4 - - + -
201A PRO* 3.1 13.9 + - + +
203A ASP* 1.3 75.9 - - - +
205A LEU* 1.3 64.8 + - - +
207A GLU* 3.3 7.9 + - - +
208A PHE* 3.1 21.0 + - + +
402A CL 3.2 27.8 - - + +
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Residues in contact with LEU 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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52A PHE* 4.1 11.7 - - + -
61A VAL* 3.8 30.1 - - + -
96A ILE* 4.1 20.6 - - + +
112A LEU* 3.9 32.1 - - + -
184A VAL* 5.2 1.1 - - + -
187A VAL* 3.9 23.3 - - + -
200A ILE* 5.1 0.8 - - + +
201A PRO 3.1 12.2 + - - +
202A SER* 3.4 12.3 - - - +
204A ARG* 1.3 77.6 - - - +
206A ARG* 1.3 63.5 + - - +
208A PHE* 3.1 15.8 + - + +
209A LEU* 2.9 30.9 + - + +
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Residues in contact with ARG 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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112A LEU* 3.4 38.3 + - + +
113A GLY 3.0 26.5 + - - -
114A ARG* 3.5 36.9 - - - +
202A SER* 2.8 14.0 + - - +
203A ASP* 2.9 33.6 + - - +
204A ARG 3.3 0.4 - - - -
205A LEU* 1.3 73.6 - - - +
207A GLU* 1.3 72.4 + - - +
209A LEU* 3.2 7.6 + - + +
210A HIS* 3.0 55.3 + - + +
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Residues in contact with GLU 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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114A ARG* 5.7 1.9 + - - -
203A ASP 3.3 14.0 + - - +
204A ARG* 3.8 8.1 - - - +
205A LEU 3.2 0.6 - - - -
206A ARG* 1.3 96.7 + - - +
208A PHE* 1.3 61.8 + - - +
210A HIS* 3.2 25.0 + - - +
211A ARG 3.2 16.5 + - - +
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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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89A ALA* 3.7 37.0 - - + -
90A VAL 4.0 5.2 - - - -
91A ASP* 3.7 37.7 - - + +
96A ILE* 3.8 22.9 - - + -
97A ALA* 4.2 9.2 - - - -
98A THR* 3.9 26.0 - - + -
204A ARG 3.1 13.1 + - - +
205A LEU* 3.1 17.4 + - + +
207A GLU* 1.3 76.1 - - - +
209A LEU* 1.3 66.6 + - + +
210A HIS 3.2 0.3 + - - -
211A ARG* 3.3 19.8 + - - +
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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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54A VAL* 4.5 17.7 - - + -
59A LEU* 4.8 12.7 - - + +
61A VAL* 4.1 5.8 - - + -
98A THR* 3.6 31.6 - - + -
112A LEU* 3.7 30.5 - - + -
205A LEU* 2.9 30.9 + - + +
206A ARG* 3.4 9.4 - - + +
208A PHE* 1.3 78.7 - - + +
210A HIS* 1.3 69.2 + - + +
211A ARG* 3.5 0.9 + - - -
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Residues in contact with HIS 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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206A ARG* 3.0 47.7 + - + +
207A GLU* 3.2 22.0 + - - +
208A PHE 3.1 0.6 - - - -
209A LEU* 1.3 85.2 - - + +
211A ARG* 1.3 65.6 + - - +
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Residues in contact with ARG 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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207A GLU 3.2 14.2 + - - +
208A PHE* 3.3 16.9 + - - +
209A LEU 4.4 0.9 - - - -
210A HIS* 1.3 81.8 - - - +
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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