Contacts of the helix formed by residues 397 - 403 (chain A) in PDB entry 1TQN
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 397 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A ASP* 3.7 21.5 - - + +
72A TRP* 4.0 24.2 - - + -
83A ALA* 4.6 0.4 - - + -
84A ILE 3.3 20.2 - - - +
85A THR* 4.3 6.5 - - + -
371A MET 4.2 2.2 - - - +
395A MET* 3.5 25.4 - - + +
396A ILE* 1.3 80.8 - - + +
398A SER* 1.3 54.2 + - - +
399A TYR 3.3 2.7 - - - -
400A ALA* 2.9 16.7 + - + -
401A LEU* 2.8 37.0 + - + +
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Residues in contact with SER 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A PRO* 4.3 10.1 - - - -
370A ALA* 6.2 0.7 - - - -
371A MET* 3.3 14.9 + - - -
373A LEU* 3.2 25.2 + - - +
396A ILE* 2.9 11.6 + - - +
397A PRO* 1.3 68.7 - - - +
399A TYR* 1.3 66.3 + - - +
400A ALA 3.1 0.2 + - - -
401A LEU* 3.1 5.5 + - - +
402A HIS* 2.8 39.2 + - - -
433A THR* 3.0 27.8 + - - -
434A PRO* 5.8 0.2 - - - -
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Residues in contact with TYR 399 (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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58A CYS* 3.2 47.8 - - + -
59A MET* 4.0 10.7 - - + +
61A ASP* 5.8 2.0 - - - +
62A MET* 3.7 19.7 - - - +
366A LEU 3.5 10.5 - - - -
368A PRO* 3.6 27.0 - - + +
371A MET* 2.9 13.8 + - - +
397A PRO 3.3 0.4 - - - -
398A SER* 1.3 77.5 - - - +
400A ALA* 1.3 63.9 + - - +
402A HIS* 3.5 3.7 + - - +
403A ARG* 2.9 65.6 + - - +
477A LEU* 3.5 23.9 - - + +
483A LEU* 4.2 13.0 - - + -
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Residues in contact with ALA 400 (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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61A ASP* 4.0 24.2 - - + +
62A MET* 2.9 27.0 - - + +
65A HIS* 4.6 13.0 + - + +
397A PRO* 2.9 25.7 + - + +
399A TYR* 1.3 77.9 - - - +
401A LEU* 1.3 66.6 + - + +
403A ARG 3.2 1.7 + - - -
404A ASP* 3.1 22.9 + - - +
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Residues in contact with LEU 401 (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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65A HIS* 4.2 14.1 - - + +
84A ILE 4.5 1.3 - - - +
85A THR* 3.7 37.9 - - + +
90A ILE* 3.8 29.2 - - + -
396A ILE* 3.9 17.9 - - + -
397A PRO* 2.8 23.2 + - + +
398A SER* 3.9 2.9 - - - +
400A ALA* 1.3 73.5 - - - +
402A HIS* 1.3 52.6 + - - +
403A ARG 3.4 0.7 + - - -
404A ASP* 3.4 13.2 + - - +
407A TYR* 5.1 2.7 - - + -
408A TRP* 2.7 27.7 + - - -
430A TYR 4.3 6.7 - - - +
431A ILE* 3.7 32.5 - - + +
433A THR* 5.9 0.2 - - - +
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Residues in contact with HIS 402 (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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364A LEU 3.5 4.9 + - - -
365A ARG* 3.1 59.9 + - + +
368A PRO* 3.6 20.8 - - + +
398A SER* 2.8 26.0 + - - +
399A TYR* 3.7 6.7 - - - +
401A LEU* 1.3 77.8 - - - +
403A ARG* 1.3 60.3 + - + +
408A TRP* 3.2 18.3 + + - +
431A ILE 3.1 19.7 + - - -
432A TYR* 3.4 12.9 - + - -
433A THR* 2.9 25.8 + - - -
434A PRO* 3.5 26.2 - - + -
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Residues in contact with ARG 403 (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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62A MET* 3.8 19.6 - - + +
365A ARG* 4.4 3.3 + - - +
366A LEU* 2.9 49.2 + - + +
367A PHE* 3.7 17.8 - - - -
399A TYR* 2.9 53.9 + - - +
400A ALA 3.2 3.6 + - - -
401A LEU 3.2 0.4 - - - -
402A HIS* 1.3 82.6 - - + +
404A ASP* 1.3 59.2 - - - +
405A PRO* 3.1 14.7 - - - +
408A TRP* 4.1 0.2 - - - -
411A PRO* 3.1 28.8 - - + +
412A GLU* 3.0 36.3 + - - +
477A LEU* 5.1 1.0 - - - +
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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