Contacts of the helix formed by residues 303 - 322 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B ILE* 3.5 1.6 - - + +
302B SER* 1.3 76.4 - - - +
304B PRO* 1.3 65.6 - - - +
305B GLU* 3.0 49.7 + - - +
306B GLU* 3.3 23.5 + - + +
307B LYS* 3.0 25.1 + - - +
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Residues in contact with PRO 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A VAL* 5.4 7.6 - - + -
465A TYR* 5.0 13.7 - - + -
302B SER 3.0 10.0 - - - +
303B ASP* 1.3 85.4 - - - +
305B GLU* 1.3 71.5 + - + +
307B LYS* 3.9 19.2 - - - +
308B ARG* 3.2 32.1 + - - +
409B ILE* 6.5 1.6 - - + -
412B LEU 5.9 0.9 - - - +
523B TRP 5.6 6.1 - - - +
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Residues in contact with GLU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A TYR* 2.6 43.4 + - + -
303B ASP* 3.0 21.7 + - - +
304B PRO* 1.3 81.2 - - + +
306B GLU* 1.3 59.4 + - - +
308B ARG* 3.4 12.8 - - - +
309B LYS* 3.1 24.1 + - - +
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Residues in contact with GLU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ILE* 3.7 27.4 - - + +
303B ASP* 3.3 23.9 + - + +
305B GLU* 1.3 77.5 - - - +
307B LYS* 1.3 56.5 + - - +
308B ARG 3.1 0.2 - - - -
309B LYS* 2.8 14.9 + - + +
310B ILE* 2.7 48.4 + - + +
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Residues in contact with LYS 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B LEU* 3.8 18.5 - - + +
301B ILE* 3.4 30.7 - - + +
302B SER 3.9 11.4 - - - -
303B ASP 3.0 13.2 + - - +
304B PRO* 3.9 17.6 - - - +
305B GLU 3.5 0.2 - - - -
306B GLU* 1.3 73.4 - - - +
308B ARG* 1.3 65.0 + - + +
310B ILE 3.4 0.2 + - - -
311B ALA* 3.1 26.9 + - - +
408B ALA* 3.0 29.3 + - + +
409B ILE* 4.8 2.8 - - - +
411B ILE* 2.7 30.3 + - - +
412B LEU 3.3 5.8 + - - -
413B GLY 3.0 19.0 + - - +
415B VAL* 4.3 16.1 - - + +
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Residues in contact with ARG 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B PRO* 3.2 17.6 + - - +
305B GLU* 3.4 14.8 - - - +
306B GLU 3.1 0.4 - - - -
307B LYS* 1.3 78.5 - - + +
309B LYS* 1.3 58.0 + - - +
311B ALA* 2.9 19.4 - - - +
312B GLY* 4.6 1.9 - - - -
403B PRO* 5.8 1.2 - - - +
405B PRO* 4.0 35.2 - - + +
409B ILE* 3.4 31.3 - - + +
522B GLU* 5.1 8.9 - - - +
523B TRP 6.0 1.8 - - - -
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Residues in contact with LYS 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B GLU 3.1 11.1 + - - +
306B GLU* 2.8 23.9 + - + +
308B ARG* 1.3 71.2 - - - +
310B ILE* 1.3 57.2 + - + +
311B ALA 2.4 20.6 - - - +
313B GLU* 3.2 48.9 + - + +
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Residues in contact with ILE 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B PHE* 6.5 0.2 - - + -
297B ALA* 3.5 45.5 - - + +
298B LEU* 3.6 20.2 - - + -
301B ILE* 4.9 7.4 - - + -
306B GLU* 2.7 38.0 + - + +
309B LYS* 1.3 70.8 - - + +
311B ALA* 1.3 67.2 + - - +
313B GLU* 3.6 15.8 - - - +
314B GLN* 3.0 29.9 + - + +
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Residues in contact with ALA 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B LEU* 4.8 9.2 - - + -
294B PHE* 4.3 22.0 - - + -
298B LEU* 4.3 5.6 - - + +
307B LYS 3.1 17.3 + - - +
308B ARG 2.9 8.9 - - - +
309B LYS 2.4 31.4 - - - +
310B ILE* 1.3 77.9 - - - +
312B GLY* 1.3 54.5 + - - +
313B GLU 2.7 4.2 + - - -
405B PRO* 4.1 26.0 - - + +
408B ALA* 5.1 1.3 - - + -
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Residues in contact with GLY 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B PHE* 4.8 0.6 - - - -
308B ARG 4.6 2.2 - - - -
311B ALA* 1.3 70.6 - - - +
313B GLU* 1.3 57.3 + - - -
314B GLN 3.3 0.2 - - - -
315B PHE* 3.4 23.3 - - - +
316B ILE* 2.8 38.3 + - - +
405B PRO* 5.9 0.2 - - - +
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Residues in contact with GLU 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B LYS* 3.2 49.8 + - + +
310B ILE* 3.6 20.7 - - - +
311B ALA 2.7 9.5 + - - -
312B GLY* 1.3 70.3 - - - +
314B GLN* 1.3 66.3 + - - +
316B ILE* 3.2 6.6 + - - +
317B ARG* 3.0 34.2 + - - +
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Residues in contact with GLN 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B ARG* 3.9 41.3 + - + +
294B PHE* 4.0 22.0 - - + -
297B ALA* 4.1 23.9 - - + +
310B ILE* 3.0 17.7 + - - +
313B GLU* 1.3 82.5 - - - +
315B PHE* 1.3 62.1 + - - +
317B ARG* 3.6 27.5 + - - +
318B VAL* 3.1 28.4 + - - +
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Residues in contact with PHE 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B GLY* 6.2 0.2 - - - -
235B SER* 3.9 30.1 - - - -
260B VAL* 3.4 31.0 - - + -
262B THR* 4.1 14.4 - - + -
294B PHE* 3.8 10.0 - + + -
312B GLY* 3.3 25.2 + - - +
313B GLU 3.2 0.4 - - - -
314B GLN* 1.3 79.6 - - - +
316B ILE* 1.3 66.2 + - + +
318B VAL* 3.4 5.5 + - - +
319B PHE* 3.3 54.1 + + - -
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Residues in contact with ILE 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B GLY* 2.8 23.0 + - - +
313B GLU* 3.7 6.3 - - - +
315B PHE* 1.3 77.6 - - + +
317B ARG* 1.3 67.8 + - - +
319B PHE* 3.0 10.2 + - + +
320B GLU* 2.9 45.3 + - + +
331B LEU* 6.2 3.4 - - + -
333B GLN* 5.5 11.7 - - - +
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Residues in contact with ARG 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B ARG* 4.0 14.4 - - - +
313B GLU* 3.0 23.4 + - - +
314B GLN* 3.6 31.8 + - - +
316B ILE* 1.3 77.9 - - - +
318B VAL* 1.3 63.5 + - - +
320B GLU* 3.1 18.6 + - - +
321B GLU* 3.1 29.2 + - - +
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Residues in contact with VAL 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B VAL* 5.6 0.2 - - + -
260B VAL* 3.6 32.1 - - + -
288B VAL* 4.3 17.0 - - + -
290B ALA* 4.7 6.5 - - + -
293B ARG* 3.1 31.2 - - - +
294B PHE* 4.4 11.2 - - + -
314B GLN 3.1 12.6 + - - +
315B PHE* 3.6 9.2 - - - +
316B ILE 3.3 0.2 - - - -
317B ARG* 1.3 78.9 - - - +
319B PHE* 1.3 63.2 + - - +
321B GLU* 3.4 11.7 + - - +
322B GLN* 3.3 28.1 + - + +
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Residues in contact with PHE 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B ILE* 3.9 20.8 - - + +
233B GLY* 3.4 35.7 - - - -
235B SER* 4.6 1.6 - - - -
258B VAL* 3.6 34.8 - - + -
260B VAL* 4.1 10.8 - - + -
315B PHE* 3.3 57.6 + + - -
316B ILE* 3.0 11.9 + - - +
318B VAL* 1.3 78.2 - - - +
320B GLU* 1.3 54.7 + - - +
322B GLN* 2.3 29.3 - - + +
323B ALA* 3.6 5.7 - - - +
331B LEU* 4.2 27.5 - - + +
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Residues in contact with GLU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ILE* 2.9 37.5 + - + +
317B ARG* 3.1 9.3 + - - +
319B PHE* 1.3 71.2 - - + +
321B GLU* 1.3 59.8 + - + +
322B GLN 2.9 12.9 - - - +
323B ALA* 3.9 3.3 - - - +
324B LYS* 3.1 26.0 + - + +
331B LEU* 5.9 4.5 - - + -
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Residues in contact with GLU 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ARG* 2.9 41.3 + - - -
317B ARG* 3.1 24.2 + - + +
318B VAL* 3.7 7.5 - - - +
320B GLU* 1.3 74.1 - - + +
322B GLN* 1.3 66.0 + - + +
324B LYS* 3.0 27.4 - - - +
325B LYS* 3.1 12.3 - - - +
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Residues in contact with GLN 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ILE* 3.9 7.9 - - + -
258B VAL* 4.6 15.2 - - + +
286B ILE* 3.9 19.2 - - - +
288B VAL* 3.8 31.4 - - + +
318B VAL* 3.3 17.1 + - + +
319B PHE* 2.3 33.6 - - + +
320B GLU 2.9 4.0 - - - +
321B GLU* 1.3 76.3 - - + +
323B ALA* 1.3 62.6 + - - +
325B LYS* 4.2 26.5 - - - +
326B LEU* 3.6 22.3 - - + +
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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