Contacts of the strand formed by residues 321 - 328 (chain A) in PDB entry 1TAQ
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 LEU 321 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309A PHE* 3.7 20.2 - - + -
310A VAL 3.7 2.9 - - - +
311A LEU* 3.9 18.5 - - + +
319A ALA 4.2 1.0 + - - -
320A ASP* 1.3 75.4 + - - +
322A LEU* 1.3 59.9 + - - +
323A ALA 3.3 20.6 - - - +
324A LEU* 4.5 3.4 - - + -
338A PRO* 3.6 38.8 - - + +
339A TYR* 3.4 22.5 + - + +
342A LEU* 3.9 36.1 - - + -
356A LEU* 3.9 7.2 - - + -
359A LEU* 4.2 18.0 - - + +
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Residues in contact with LEU 322 (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 HIS* 3.8 30.5 - - + +
310A VAL* 2.6 18.4 + - + +
311A LEU 3.9 4.9 - - - +
312A SER* 3.7 28.7 - - - +
320A ASP* 3.0 31.8 + - - +
321A LEU* 1.3 72.7 - - - +
323A ALA* 1.3 60.2 + - + +
338A PRO* 3.7 10.0 - - - +
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Residues in contact with ALA 323 (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 HIS* 5.9 2.2 - - - +
309A PHE* 3.2 3.3 - - - -
310A VAL* 2.9 37.8 + - + -
321A LEU* 3.3 9.2 - - - +
322A LEU* 1.3 80.7 - - + +
324A LEU* 1.3 60.0 + - - +
338A PRO* 3.7 8.1 - - - -
402A ALA* 3.7 19.3 - - + +
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Residues in contact with LEU 324 (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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299A TRP* 4.5 8.7 - - + -
307A VAL* 4.4 6.7 - - + -
308A GLY 3.5 15.7 - - - +
309A PHE* 3.9 12.6 - - + -
321A LEU* 4.5 2.7 - - + -
323A ALA* 1.3 75.2 - - - +
325A ALA* 1.3 66.5 + - - +
334A ARG* 4.1 1.0 - - - +
335A ALA* 3.0 28.5 + - + +
338A PRO* 3.5 39.4 - - + +
341A ALA* 4.0 9.9 - - + +
342A LEU* 3.7 28.9 - - + +
345A LEU* 4.2 9.4 - - + -
356A LEU* 3.9 21.3 - - + -
402A ALA* 4.1 1.3 - - - -
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Residues in contact with ALA 325 (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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299A TRP* 4.2 4.4 - - - -
307A VAL* 3.3 8.3 - - - +
308A GLY 2.9 29.3 + - - +
324A LEU* 1.3 75.7 - - - +
326A ALA* 1.3 62.7 + - - +
332A VAL* 4.3 1.6 - - + -
333A HIS 3.3 13.5 - - - +
334A ARG* 4.0 11.4 - - + +
402A ALA* 3.5 31.2 - - + +
403A GLY* 3.5 12.6 - - - +
406A ALA* 4.4 0.7 - - + -
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Residues in contact with ALA 326 (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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299A TRP* 4.0 8.7 - - + -
301A PRO* 3.4 39.5 - - + -
305A ALA* 4.2 5.2 - - + -
306A PHE 3.2 11.7 - - - +
307A VAL* 4.7 5.4 - - + -
325A ALA* 1.3 76.2 - - - +
327A ALA* 1.3 61.8 + - - +
331A ARG 3.8 0.3 - - - +
332A VAL* 3.4 4.9 - - - +
333A HIS* 2.8 33.8 + - - +
406A ALA* 4.1 3.4 - - - -
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Residues in contact with ALA 327 (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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305A ALA* 3.0 6.7 - - - +
306A PHE* 2.8 34.7 + - - +
326A ALA* 1.3 75.4 - - - +
328A ARG* 1.3 62.2 + - - +
330A GLY 5.2 2.2 - - - -
331A ARG 3.6 7.6 - - - +
332A VAL* 4.7 5.8 - - + -
333A HIS* 5.2 0.4 - - - -
406A ALA* 3.8 9.0 - - + +
407A ALA* 3.7 35.9 - - + +
410A GLU* 4.3 12.8 - - + +
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Residues in contact with ARG 328 (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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302A PRO* 4.1 34.5 - - + +
303A GLU 3.7 16.0 + - - -
304A GLY* 4.2 16.3 + - - +
305A ALA* 3.5 28.5 - - + +
327A ALA* 1.3 71.8 - - - +
329A GLY* 1.3 62.5 + - - +
330A GLY 3.0 7.5 + - - +
331A ARG* 3.1 32.5 + - - +
333A HIS* 4.6 4.7 - - + -
410A GLU* 3.6 6.3 - - - -
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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