Contacts of the helix formed by residues 296 - 305 (chain A) in PDB entry 1TFR
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 296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290A PHE 5.0 0.2 - - - -
291A VAL* 4.5 17.2 + - - +
294A GLY* 3.3 10.1 + - - -
295A LEU* 1.3 71.8 - - - +
297A LYS* 1.3 66.1 + - - +
298A LEU 3.0 1.8 - - - -
299A THR* 2.4 35.6 + - - +
300A ASN* 4.1 0.9 + - - +
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Residues in contact with LYS 297 (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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295A LEU 3.3 1.4 - - - -
296A SER* 1.3 77.3 - - - +
298A LEU* 1.3 53.9 + - + +
300A ASN* 2.4 44.6 + - - +
301A SER* 4.0 0.2 + - - -
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Residues in contact with LEU 298 (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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45A HIS* 5.8 2.2 - - + +
48A LEU* 3.9 36.6 - - + -
49A ASN* 4.3 13.9 - - - +
52A LYS* 4.2 15.7 - - + +
290A PHE* 3.4 25.6 - - + -
295A LEU* 3.1 27.1 - - + +
297A LYS* 1.3 79.6 - - + +
299A THR* 1.3 56.2 + - - +
300A ASN 3.0 3.1 - - - -
301A SER* 2.7 37.4 + - - +
302A ILE 3.6 0.7 + - - -
305A PHE* 3.9 22.9 - - + -
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Residues in contact with THR 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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287A TYR* 3.3 39.2 + - + +
290A PHE* 4.0 16.4 - - + -
291A VAL* 3.7 18.8 - - + -
295A LEU 3.5 0.2 + - - -
296A SER* 2.4 34.1 + - - +
298A LEU* 1.3 78.0 - - - +
300A ASN* 1.3 58.1 + - - +
301A SER 3.0 5.4 + - - -
302A ILE* 3.5 24.0 + - - +
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Residues in contact with ASN 300 (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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296A SER 4.1 0.6 + - - +
297A LYS* 2.4 44.1 + - - +
298A LEU 3.0 1.2 - - - -
299A THR* 1.3 80.7 + - - +
301A SER* 1.3 78.3 + - - +
302A ILE 3.7 0.7 - - - -
303A ASN* 3.7 11.1 + - - -
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Residues in contact with SER 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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52A LYS* 4.4 11.0 + - - +
297A LYS* 4.0 2.1 + - - -
298A LEU* 2.7 19.1 + - - +
300A ASN* 1.3 100.4 + - - +
302A ILE* 1.3 55.7 + - - +
303A ASN* 3.0 12.6 - - - +
304A GLU* 2.8 48.5 + - - +
305A PHE* 3.3 8.0 - - - -
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Residues in contact with ILE 302 (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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283A ARG* 3.0 31.8 + - - +
286A ILE* 3.9 24.7 - - + -
287A TYR* 3.4 54.3 - - + +
290A PHE* 3.7 24.9 - - + -
298A LEU 4.0 0.2 - - - +
299A THR* 3.5 18.4 + - - +
300A ASN 3.7 0.8 - - - -
301A SER* 1.3 77.1 - - - +
303A ASN* 1.3 62.0 + - - +
305A PHE* 3.1 15.3 + - - +
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Residues in contact with ASN 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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59A LYS* 5.7 0.7 + - - -
283A ARG* 4.6 3.5 + - - +
300A ASN 3.7 9.3 + - - -
301A SER* 3.0 19.0 - - - +
302A ILE* 1.3 81.7 - - - +
304A GLU* 1.3 70.2 + - - +
305A PHE 3.2 6.3 + - - +
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Residues in contact with GLU 304 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A LYS* 3.7 43.6 - - + +
55A VAL* 3.9 13.7 - - - +
56A LYS* 4.7 22.6 + - + +
59A LYS* 6.4 0.2 - - - -
301A SER* 2.8 34.9 + - - +
303A ASN* 1.3 93.9 + - - +
305A PHE* 1.3 59.7 + - - +
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Residues in contact with PHE 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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48A LEU* 3.4 31.2 - - + -
51A ILE* 4.1 6.7 - - + -
52A LYS* 3.7 31.2 - - + -
55A VAL* 3.6 12.6 - - - +
59A LYS* 4.0 8.0 + - - -
119A MET* 3.4 26.2 - - + -
120A PRO* 4.6 0.2 - - - -
121A TYR* 3.0 46.2 + - + +
283A ARG* 2.5 43.7 + - - +
286A ILE* 4.7 7.2 - - + -
290A PHE* 3.6 31.2 - + + -
298A LEU* 3.9 16.2 - - + -
301A SER 3.3 25.6 - - - -
302A ILE* 3.1 12.6 + - - +
303A ASN 3.7 4.7 - - - +
304A GLU* 1.3 81.4 - - - +
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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