Contacts of the helix formed by residues 328 - 336 (chain A) in PDB entry 1QTI
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 GLY 328 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327A GLU* 1.3 79.4 - - - +
329A SER* 1.3 64.1 + - - +
331A PHE* 2.8 18.2 + - - +
332A LEU* 3.1 15.7 + - - +
392A ASP* 3.2 11.8 + - - -
395A VAL* 3.3 32.0 - - - +
396A GLY* 3.6 6.6 - - - -
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Residues in contact with SER 329 (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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326A ASP 3.7 6.0 + - - -
327A GLU 3.5 0.4 - - - -
328A GLY* 1.3 71.5 - - - +
330A PHE* 1.3 64.2 + - - +
332A LEU* 3.4 3.0 + - - +
333A LEU* 3.1 24.8 + - - +
392A ASP* 2.6 32.7 + - - -
435A TRP* 3.8 13.9 - - - -
436A MET* 2.9 46.7 + - - +
439A ILE* 3.8 6.9 - - - +
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Residues in contact with PHE 330 (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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80A GLY 4.4 0.2 - - - -
81A SER* 5.3 0.7 - - - -
84A TRP* 4.1 7.6 - + - -
327A GLU 4.1 1.0 + - - -
328A GLY 3.0 2.6 + - - -
329A SER* 1.3 78.8 + - - +
331A PHE* 1.3 79.4 + + + +
333A LEU* 3.8 0.9 + - - +
334A TYR* 3.4 52.2 + + - +
432A TRP* 3.7 26.0 - + - -
436A MET* 3.8 10.1 - - + -
439A ILE* 3.1 30.0 - - + +
440A HIS* 3.7 13.7 - - + -
442A TYR* 3.9 17.5 - + - -
600A GNT 4.0 38.1 - - + -
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Residues in contact with PHE 331 (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 ILE* 3.5 21.9 - - + +
288A PHE* 3.3 56.5 - + + +
290A PHE* 4.3 4.0 - + - -
327A GLU 3.3 21.3 - - - -
328A GLY 2.8 11.5 + - - +
330A PHE* 1.3 81.3 - + + +
332A LEU* 1.3 65.5 + - - +
333A LEU 3.3 0.2 - - - -
334A TYR* 3.5 4.9 + - - +
335A GLY 3.2 16.5 + - - -
395A VAL* 4.1 5.6 - - + -
440A HIS* 3.8 18.6 - + + -
600A GNT 3.4 56.1 - + - -
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Residues in contact with LEU 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ILE* 5.3 3.6 - - + -
328A GLY 3.1 10.7 + - - +
329A SER* 4.0 5.6 - - - +
331A PHE* 1.3 74.5 - - - +
333A LEU* 1.3 66.9 + - - +
334A TYR 3.1 0.2 - - - -
336A ALA* 2.9 51.6 + - + +
339A PHE* 3.5 30.2 - - + +
355A GLY* 5.0 1.3 - - - -
359A SER* 4.5 4.7 - - - +
391A LEU* 3.2 48.9 - - + +
392A ASP* 3.5 14.8 - - + +
395A VAL* 3.7 24.2 - - + -
435A TRP* 5.4 0.7 - - + -
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Residues in contact with LEU 333 (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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74A GLN* 5.2 3.1 + - - -
75A PHE* 4.0 11.8 - - + -
329A SER 3.1 17.7 + - - +
330A PHE 3.8 2.5 - - - +
331A PHE 3.3 0.2 - - - -
332A LEU* 1.3 78.6 - - - +
334A TYR* 1.3 74.3 + - + +
336A ALA 5.4 0.3 - - - +
339A PHE* 3.8 16.1 - - - +
340A SER* 3.5 10.5 - - - -
341A LYS* 3.3 35.0 - - + +
432A TRP* 3.2 35.7 - - + -
435A TRP* 3.8 17.1 - - + -
436A MET* 3.4 17.5 - - + -
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Residues in contact with TYR 334 (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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72A ASP* 2.6 32.0 + - - -
74A GLN* 3.4 36.6 + - + +
75A PHE* 3.6 25.5 - + - -
81A SER* 3.4 18.4 - - - -
330A PHE* 3.4 44.0 + + - +
331A PHE* 3.5 6.3 + - - +
332A LEU 3.1 0.8 - - - -
333A LEU* 1.3 91.0 - - + +
335A GLY* 1.3 57.2 + - - +
432A TRP* 3.9 1.4 - + - -
600A GNT 4.4 10.0 - - - -
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Residues in contact with GLY 335 (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 ILE* 3.5 24.5 - - - +
331A PHE 3.2 8.1 + - - -
332A LEU 3.3 0.2 + - - -
334A TYR* 1.3 79.8 - - - +
336A ALA* 1.3 61.0 + - - +
337A PRO* 3.9 2.4 - - - +
358A LEU* 3.3 16.6 - - - +
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Residues in contact with ALA 336 (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 ILE* 4.4 2.2 - - + +
332A LEU* 2.9 28.5 + - + +
333A LEU 5.4 0.5 - - - +
335A GLY* 1.3 78.4 - - - +
337A PRO* 1.3 72.0 - - + +
338A GLY 3.4 0.2 + - - -
339A PHE* 3.2 45.0 + - + +
351A ASP 5.9 0.2 - - - +
355A GLY* 4.7 8.1 - - - -
358A LEU* 4.0 8.1 - - + -
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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