Contacts of the helix formed by residues 318 - 330 (chain A) in PDB entry 1T8U
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 ASP 318 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314A ARG* 2.6 48.4 + - + +
317A SER* 1.3 77.6 + - - +
319A PRO* 1.3 66.1 - - - +
320A ALA* 3.8 6.6 + - - +
321A GLY* 3.0 29.0 + - - -
322A GLU 3.2 8.7 + - - -
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Residues in contact with PRO 319 (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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171A PHE* 4.2 8.1 - - + -
314A ARG 3.5 1.3 - - - +
315A LEU* 3.5 26.5 - - + +
316A ILE 3.8 6.1 - - - +
317A SER 3.7 5.6 - - - +
318A ASP* 1.3 89.1 - - - +
320A ALA* 1.3 58.7 + - + +
321A GLY 3.3 0.2 + - - -
322A GLU* 3.4 0.7 + - - -
323A LEU* 2.9 34.7 + - - +
341A PHE* 3.6 48.2 - - + -
350A PRO* 4.4 11.4 - - + -
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Residues in contact with ALA 320 (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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318A ASP* 3.3 6.1 + - - +
319A PRO* 1.3 80.7 - - + +
321A GLY* 1.3 62.7 + - - +
323A LEU* 3.8 4.4 - - - +
324A GLY* 2.9 21.0 + - - -
336A ILE 4.8 3.4 - - - +
337A THR* 3.6 11.0 - - - +
338A ASP* 3.4 39.7 - - + +
341A PHE* 3.6 8.8 - - + -
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Residues in contact with GLY 321 (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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314A ARG* 5.3 2.5 - - - -
318A ASP* 3.0 29.3 + - - -
320A ALA* 1.3 76.0 - - - +
322A GLU* 1.3 64.8 + - - +
324A GLY* 3.0 12.3 + - - -
325A ARG* 3.4 14.1 + - - +
334A ARG* 5.5 0.7 + - - -
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Residues in contact with GLU 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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310A VAL* 3.6 15.7 - - + +
311A SER* 3.0 24.9 + - - +
314A ARG* 2.9 47.9 - - + +
315A LEU* 3.7 22.0 - - + +
318A ASP 3.2 5.1 + - - +
319A PRO 4.0 5.2 - - - +
321A GLY* 1.3 74.0 - - - +
323A LEU* 1.3 62.9 + - + +
325A ARG* 2.8 45.3 + - - +
326A VAL* 3.0 25.8 + - + +
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Residues in contact with LEU 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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168A LEU* 4.1 15.7 - - + -
171A PHE* 4.0 26.0 - - + -
172A LEU* 3.6 31.4 - - + +
315A LEU* 3.8 25.6 - - + -
319A PRO 2.9 26.5 + - - +
320A ALA 3.9 4.0 - - - +
321A GLY 3.3 0.2 - - - -
322A GLU* 1.3 77.6 - - - +
324A GLY* 1.3 57.9 + - - +
326A VAL* 3.7 3.5 - - + +
327A GLN* 2.9 39.9 + - - +
336A ILE* 3.9 37.2 - - + -
341A PHE* 4.5 1.8 - - + -
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Residues in contact with GLY 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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320A ALA 2.9 15.0 + - - -
321A GLY 3.0 5.5 + - - -
323A LEU* 1.3 78.9 - - - +
325A ARG* 1.3 61.6 + - - +
327A GLN* 3.3 11.0 + - - +
328A ASP* 3.1 27.2 + - - +
334A ARG* 3.5 28.9 + - - -
336A ILE 5.5 0.4 - - - -
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Residues in contact with ARG 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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308A LEU* 4.0 24.8 - - + +
309A PHE 3.3 26.0 + - - +
310A VAL* 4.3 1.9 - - + +
311A SER* 4.2 4.8 - - - +
321A GLY 3.4 10.1 + - - +
322A GLU* 2.8 46.0 + - - +
324A GLY* 1.3 76.2 - - - +
326A VAL* 1.3 58.7 + - + +
328A ASP* 3.3 9.5 + - - +
329A PHE* 2.9 29.8 + - - +
334A ARG* 4.0 5.3 - - - +
400A HIS* 5.0 21.7 + - - +
402A PHE* 5.0 0.8 - - - -
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Residues in contact with VAL 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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168A LEU* 4.2 16.4 - - + -
172A LEU* 3.7 30.3 - - + -
239A ILE* 4.1 11.7 - - + -
308A LEU* 3.6 9.9 - - + -
310A VAL* 3.7 30.7 - - + -
322A GLU 3.0 17.1 + - - +
323A LEU* 3.7 8.7 - - - +
325A ARG* 1.3 77.2 - - + +
327A GLN* 1.3 57.1 + - - +
329A PHE* 3.3 2.6 + - - +
330A LEU* 2.9 42.0 + - + +
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Residues in contact with GLN 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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172A LEU* 4.6 14.1 - - + -
175A HIS* 3.2 21.4 - - + -
323A LEU 2.9 33.9 + - - +
324A GLY* 3.8 8.9 - - - +
326A VAL* 1.3 75.6 - - - +
328A ASP* 1.3 61.8 + - - +
330A LEU* 3.4 2.3 + - - -
331A GLY 3.0 3.5 + - - -
332A LEU* 2.7 49.8 + - + +
333A LYS 3.3 0.6 - - - +
334A ARG* 4.0 11.2 - - + +
335A ILE 3.0 24.0 + - - -
336A ILE* 3.0 41.6 + - - +
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Residues in contact with ASP 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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324A GLY 3.1 10.6 + - - +
325A ARG* 3.7 8.6 - - - +
327A GLN* 1.3 74.5 - - - +
329A PHE* 1.3 64.4 + - - +
331A GLY* 2.9 15.9 + - - -
332A LEU 4.5 4.7 - - - +
334A ARG* 2.6 50.2 + - - +
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Residues in contact with PHE 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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237A LYS* 3.4 49.0 + - + -
238A LEU 3.8 5.4 - - - -
239A ILE* 3.8 16.4 - - + -
305A ARG 3.5 23.1 - - - -
306A GLN* 3.5 26.7 - - - -
307A MET 4.0 3.8 - - - -
308A LEU* 3.6 43.7 - - + -
325A ARG 2.9 17.9 + - - +
326A VAL 3.3 3.6 + - - +
328A ASP* 1.3 77.2 - - - +
330A LEU* 1.3 71.4 + - + +
331A GLY 3.3 0.7 + - - -
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Residues in contact with LEU 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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155A ALA* 3.6 26.9 - - + -
172A LEU* 3.8 28.7 - - + -
211A ILE* 3.3 23.5 - - + +
213A MET* 4.0 12.6 - - - -
237A LYS* 4.1 16.2 - - + -
239A ILE* 4.1 7.2 - - + -
326A VAL* 2.9 28.0 + - + +
327A GLN 4.0 0.9 - - - +
329A PHE* 1.3 97.0 - - + +
331A GLY* 1.3 61.3 + - - +
332A LEU* 3.9 24.5 - - + -
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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