Contacts of the helix formed by residues 303 - 322 (chain A) in PDB entry 3TQI
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 303 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A ILE* 3.6 1.8 - - + +
302A SER* 1.3 75.5 - - - +
304A PRO* 1.3 73.9 - - - +
305A GLU* 3.2 20.6 + - - +
306A GLU* 2.8 43.4 + - + +
307A LYS* 3.1 20.8 + - - +
465B TYR* 5.0 5.4 + - - -
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Residues in contact with PRO 304 (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 SER 3.1 6.0 - - - +
303A ASP* 1.3 90.7 - - - +
305A GLU* 1.3 68.8 + - + +
307A LYS* 3.5 23.6 + - - +
308A ARG* 3.3 29.0 + - - +
409A ILE* 6.4 1.6 - - + -
412A LEU 5.8 1.3 - - - +
523A TRP 5.4 7.0 - - - +
456B VAL* 5.4 9.6 - - + -
465B TYR* 5.0 16.4 - - + -
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Residues in contact with GLU 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ASP* 3.2 13.7 + - - +
304A PRO* 1.3 83.8 - - + +
306A GLU* 1.3 62.9 + - - +
308A ARG* 3.5 14.2 + - - +
309A LYS* 3.3 19.4 + - - +
465B TYR* 3.1 33.9 + - + -
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Residues in contact with GLU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ILE* 4.0 24.1 - - + +
303A ASP* 2.8 29.4 + - + +
305A GLU* 1.3 76.7 - - - +
307A LYS* 1.3 63.1 + - - +
309A LYS* 3.7 14.8 - - + +
310A ILE* 3.0 47.5 + - + +
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Residues in contact with LYS 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 4.0 11.7 - - + +
301A ILE* 3.6 28.7 - - + +
302A SER 3.9 8.5 - - - -
303A ASP 3.1 13.4 + - - +
304A PRO* 3.6 27.5 - - - +
305A GLU 3.3 0.2 - - - -
306A GLU* 1.3 76.6 - - - +
308A ARG* 1.3 58.1 + - + +
311A ALA* 3.0 35.2 + - - +
405A PRO* 5.6 0.4 - - - -
408A ALA* 3.0 27.9 + - + +
409A ILE* 4.8 3.0 - - - +
411A ILE* 2.6 32.5 + - - +
412A LEU 3.5 4.6 + - - -
413A GLY 3.1 13.8 + - - +
415A VAL* 4.1 15.9 - - + +
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Residues in contact with ARG 308 (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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304A PRO* 3.3 16.5 + - - +
305A GLU* 3.6 16.8 - - - +
307A LYS* 1.3 80.3 - - + +
309A LYS* 1.3 54.5 + - - +
311A ALA 2.4 21.3 - - - +
312A GLY* 4.5 1.2 - - - -
403A PRO* 5.6 1.0 - - - +
405A PRO* 3.6 38.7 - - + +
409A ILE* 3.2 32.3 - - + +
522A GLU* 5.1 8.9 - - - +
523A TRP 6.3 0.4 - - - -
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Residues in contact with LYS 309 (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 GLU 3.3 11.1 + - - +
306A GLU* 3.7 17.2 - - - +
307A LYS 3.2 0.6 - - - -
308A ARG* 1.3 77.5 - - - +
310A ILE* 1.3 74.4 + - + +
311A ALA 3.1 1.7 - - - +
312A GLY 4.0 0.3 - - - -
313A GLU* 3.0 49.4 + - + +
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Residues in contact with ILE 310 (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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294A PHE* 6.4 0.4 - - + -
297A ALA* 3.0 42.6 - - + +
298A LEU* 3.7 18.6 - - + -
301A ILE* 4.9 7.4 - - + -
306A GLU* 3.0 42.4 + - + +
309A LYS* 1.3 89.2 - - + +
311A ALA* 1.3 59.6 + - - +
313A GLU* 3.5 15.3 - - - +
314A GLN* 3.0 35.7 + - + +
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Residues in contact with ALA 311 (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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264A LEU* 4.3 24.0 - - + -
294A PHE* 4.3 12.6 - - + -
298A LEU* 4.5 11.2 - - + -
307A LYS 3.0 15.8 + - - +
308A ARG* 2.4 30.7 - - - +
309A LYS 3.1 0.9 - - - +
310A ILE* 1.3 76.9 - - - +
312A GLY* 1.3 57.8 + - - +
405A PRO* 4.7 20.2 - - + +
408A ALA* 4.7 2.7 - - + -
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Residues in contact with GLY 312 (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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294A PHE* 4.6 1.8 - - - -
308A ARG 4.5 1.3 - - - -
309A LYS 4.0 0.2 - - - -
310A ILE 3.4 1.2 + - - -
311A ALA* 1.3 73.7 - - - +
313A GLU* 1.3 59.3 + - - +
315A PHE* 3.4 24.5 - - - +
316A ILE* 2.8 33.1 + - - +
405A PRO* 6.4 0.2 - - - -
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Residues in contact with GLU 313 (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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309A LYS* 3.0 44.9 + - + +
310A ILE* 3.5 16.9 - - - +
312A GLY* 1.3 73.8 - - - +
314A GLN* 1.3 60.6 + - - +
315A PHE 3.0 0.2 - - - -
316A ILE* 3.0 10.3 + - - +
317A ARG* 3.0 42.9 + - - +
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Residues in contact with GLN 314 (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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293A ARG* 3.3 42.3 + - + +
294A PHE* 3.8 23.9 - - + -
297A ALA* 4.1 26.7 - - + +
310A ILE* 3.0 18.5 + - + +
313A GLU* 1.3 79.8 - - - +
315A PHE* 1.3 57.2 + - - +
317A ARG* 3.8 26.9 + - - +
318A VAL* 2.9 31.9 + - - +
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Residues in contact with PHE 315 (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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233A GLY* 6.0 0.2 - - - -
235A SER* 4.1 24.2 - - - -
260A VAL* 3.7 23.3 - - + -
262A THR* 4.1 19.7 - - + -
294A PHE* 3.8 6.4 - + + -
312A GLY* 3.4 26.8 - - - +
314A GLN* 1.3 77.7 - - - +
316A ILE* 1.3 68.9 + - + +
318A VAL* 3.2 5.4 + - + +
319A PHE* 3.2 53.1 + + - -
404A GLY 6.1 1.6 - - - -
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Residues in contact with ILE 316 (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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312A GLY 2.8 26.0 - - - +
313A GLU* 3.0 6.8 + - - +
315A PHE* 1.3 80.2 - - + +
317A ARG* 1.3 63.3 + - - +
319A PHE* 3.3 9.6 + - + +
320A GLU* 2.9 45.3 + - + +
331A LEU* 5.4 6.1 - - + -
333A GLN* 5.3 12.1 - - - +
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Residues in contact with ARG 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ARG* 4.1 20.0 - - - +
313A GLU* 3.0 30.8 + - - +
314A GLN* 3.8 31.0 + - - +
316A ILE* 1.3 76.0 - - - +
318A VAL* 1.3 61.9 + - - +
320A GLU* 3.1 12.5 + - - +
321A GLU* 3.0 30.9 + - + +
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Residues in contact with VAL 318 (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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260A VAL* 3.8 30.7 - - + -
288A VAL* 4.3 18.4 - - + -
290A ALA* 4.8 5.4 - - + -
293A ARG* 3.7 31.9 - - - +
294A PHE* 4.4 11.0 - - + -
314A GLN 2.9 22.7 - - - +
315A PHE* 3.2 8.2 + - - +
317A ARG* 1.3 74.7 - - - +
319A PHE* 1.3 58.8 + - - +
321A GLU* 3.3 10.7 + - + +
322A GLN* 3.1 33.9 + - + +
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Residues in contact with PHE 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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231A ILE* 4.1 20.0 - - + +
233A GLY* 3.4 37.5 - - - -
235A SER* 4.0 9.4 - - - -
258A VAL* 3.9 22.7 - - + -
260A VAL* 4.0 18.8 - - + -
315A PHE* 3.2 58.4 + + - +
316A ILE* 3.8 9.9 - - + +
318A VAL* 1.3 81.3 - - + +
320A GLU* 1.3 54.3 + - + +
322A GLN* 2.4 25.2 - - + +
323A ALA* 3.6 5.7 - - - +
331A LEU* 4.4 26.5 - - + +
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Residues in contact with GLU 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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316A ILE* 2.9 38.7 + - + +
317A ARG* 3.1 9.5 + - - +
319A PHE* 1.3 75.4 - - - +
321A GLU* 1.3 66.1 + - + +
322A GLN 3.2 1.8 - - - +
323A ALA* 3.8 3.0 - - - +
324A LYS* 3.0 29.0 + - - +
331A LEU* 6.2 3.6 - - + -
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Residues in contact with GLU 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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293A ARG* 2.9 42.2 + - - -
317A ARG* 3.0 18.9 + - + +
318A VAL* 3.6 10.0 - - - +
320A GLU* 1.3 73.4 - - + +
322A GLN* 1.3 67.1 + - + +
324A LYS* 3.2 15.7 - - - +
325A LYS* 3.1 25.7 - - + +
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Residues in contact with GLN 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ILE* 4.0 8.0 - - + +
258A VAL* 4.4 15.4 - - + +
286A ILE* 4.2 15.8 - - - +
288A VAL* 3.3 41.8 - - + +
318A VAL* 3.1 18.4 + - + +
319A PHE* 2.4 24.8 - - + +
320A GLU 3.2 1.6 - - - +
321A GLU* 1.3 75.4 - - + +
323A ALA* 1.3 70.1 + - - +
325A LYS* 4.3 22.7 - - - +
326A LEU* 3.8 21.9 - - + +
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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