Contacts of the helix formed by residues 298 - 308 (chain A) in PDB entry 5TQW
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 PRO 298 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204A TYR* 4.0 24.2 - - + +
288A GLY 5.0 0.2 - - - -
289A GLY 3.3 26.2 - - - +
290A PRO 3.6 7.4 - - - +
291A VAL* 3.8 16.8 - - + -
296A LYS 4.8 0.4 - - - +
297A GLN* 1.3 89.4 - - - +
299A ARG* 1.3 65.7 + - - +
300A CYS* 4.2 4.7 - - + +
301A PHE* 3.1 42.4 + - + +
302A VAL* 3.2 10.2 + - - +
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Residues in contact with ARG 299 (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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274A ASN* 4.4 17.0 + - - +
278A LEU* 3.8 23.1 - - + +
289A GLY* 3.6 15.7 - - - -
290A PRO* 3.4 26.1 + - + +
292A ASP* 5.9 1.6 - - + -
298A PRO* 1.3 69.8 - - - +
300A CYS* 1.3 58.8 + - - +
301A PHE 3.4 0.2 - - - -
302A VAL* 3.6 11.3 - - + +
303A LEU* 2.9 47.6 + - + +
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Residues in contact with CYS 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A TYR* 5.4 3.1 - - + -
275A TRP* 3.0 32.1 + - - +
278A LEU* 3.7 21.1 - - - -
279A MET* 3.7 24.9 - - + -
288A GLY* 3.6 12.6 - - - -
289A GLY 3.3 25.4 - - - +
298A PRO* 4.7 7.9 - - + -
299A ARG* 1.3 76.2 - - - +
301A PHE* 1.3 60.6 + - + +
303A LEU 3.2 1.0 + - - -
304A MET* 3.0 24.4 + - - +
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Residues in contact with PHE 301 (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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129A GLY 4.3 0.9 - - - -
132A ILE* 4.1 25.1 - - + -
133A ARG* 2.5 75.1 + - + +
136A HIS* 4.5 7.0 - - + -
204A TYR* 4.3 21.5 - + - -
279A MET* 5.9 1.8 - - + -
296A LYS 5.8 0.2 - - - -
297A GLN* 3.1 25.4 - - + +
298A PRO* 3.1 34.9 + - + +
300A CYS* 1.3 82.7 - - + +
302A VAL* 1.3 57.3 + - - +
304A MET* 3.5 19.7 - - - -
305A ASP* 2.9 16.5 + - - -
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Residues in contact with VAL 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ASP* 4.7 13.5 - - + +
295A LEU* 4.4 23.6 - - + -
297A GLN* 3.3 24.7 - - + +
298A PRO 3.2 18.3 + - - +
299A ARG* 3.6 12.3 - - + +
300A CYS 3.2 0.2 - - - -
301A PHE* 1.3 77.5 - - - +
303A LEU* 1.3 56.8 + - + +
305A ASP* 3.1 8.8 + - + +
306A HIS* 2.9 47.6 + - + +
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Residues in contact with LEU 303 (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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271A PRO* 4.0 19.7 - - + +
274A ASN* 4.3 8.3 - - + -
275A TRP* 3.8 34.5 - - + +
278A LEU* 3.7 29.6 - - + -
299A ARG* 2.9 36.5 + - + +
300A CYS 3.2 4.2 + - - +
302A VAL* 1.3 75.9 - - + +
304A MET* 1.3 59.0 + - - +
306A HIS* 3.0 28.0 + - + +
307A ILE* 2.9 33.6 + - + +
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Residues in contact with MET 304 (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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125A LEU* 3.7 29.9 - - + +
129A GLY* 3.7 30.3 - - - -
133A ARG* 3.4 15.7 - - - +
207A PHE* 3.8 13.0 - - + -
272A MET* 5.8 0.4 - - - -
275A TRP* 3.4 35.7 - - + +
279A MET* 5.2 0.7 - - - -
300A CYS* 3.0 12.7 + - - +
301A PHE* 3.5 32.5 - - + +
302A VAL 3.3 0.2 - - - -
303A LEU* 1.3 74.8 - - - +
305A ASP* 1.3 58.9 + - - +
307A ILE* 3.3 11.0 + - + +
308A LEU* 3.0 32.6 + - + +
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Residues in contact with ASP 305 (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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133A ARG* 2.7 29.2 + - - -
295A LEU* 5.5 5.1 - - + +
297A GLN* 2.8 34.6 + - - +
301A PHE 2.9 11.1 + - - -
302A VAL* 3.1 9.6 + - + +
304A MET* 1.3 75.4 - - - +
306A HIS* 1.3 61.8 + - + +
308A LEU* 3.3 10.6 + - - +
309A ASN* 2.6 40.6 + - - +
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Residues in contact with HIS 306 (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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271A PRO* 5.6 4.7 - - + +
302A VAL* 2.9 39.1 + - + +
303A LEU* 3.0 30.9 + - + +
305A ASP* 1.3 81.7 - - + +
307A ILE* 1.3 59.3 + - + +
309A ASN* 2.9 12.3 + - - +
310A LEU* 2.9 38.3 + - + +
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Residues in contact with ILE 307 (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 LEU* 3.7 34.7 - - + +
125A LEU* 5.2 8.1 - - + -
268A ILE* 3.8 16.6 - - + +
271A PRO* 3.7 26.5 - - + -
272A MET* 3.8 27.8 - - + +
303A LEU* 2.9 16.4 + - + +
304A MET* 3.3 9.4 + - - +
306A HIS* 1.3 75.3 - - - +
308A LEU* 1.3 65.0 + - + +
309A ASN 3.2 0.9 + - - -
310A LEU* 3.4 36.2 + - + +
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Residues in contact with LEU 308 (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 LEU* 4.9 7.2 - - + +
125A LEU* 5.8 4.5 - - + -
126A SER* 3.7 42.0 - - - +
133A ARG* 4.8 9.0 - - - +
304A MET* 3.0 19.4 + - + +
305A ASP* 3.7 16.8 - - - +
306A HIS 3.2 0.2 - - - -
307A ILE* 1.3 78.1 - - + +
309A ASN* 1.3 63.5 + - - +
310A LEU 3.6 0.4 - - - -
311A LYS* 4.9 9.4 - - - +
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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