Contacts of the helix formed by residues 302 - 321 (chain B) in PDB entry 4QGC
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 PRO 302 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B HIS* 6.1 2.5 - - + -
298B GLY 5.2 0.2 - - - +
300B GLU 3.7 6.5 - - - +
301B ILE* 1.3 103.7 - - + +
303B ALA* 1.3 65.5 + - - +
304B GLU* 4.0 22.7 - - + +
305B LYS* 3.1 27.5 + - + -
306B VAL* 3.3 3.5 - - - +
339C ARG* 4.5 13.5 - - - +
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Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B GLY* 5.2 2.5 + - - -
301B ILE 3.7 1.2 + - - -
302B PRO* 1.3 72.0 - - - +
304B GLU* 1.3 58.6 + - - +
305B LYS 3.1 4.9 + - - -
306B VAL* 3.6 18.0 + - - +
307B PHE* 4.5 4.9 + - - -
339C ARG* 5.2 5.3 - - - +
340C PRO* 4.0 20.0 - - + +
341C THR 3.4 33.4 - - - +
342C ARG* 3.8 10.8 - - + +
345C GLY* 4.3 13.5 - - - -
346C SER 4.9 0.3 + - - -
377C MET* 6.1 0.2 - - - -
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Residues in contact with GLU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B PRO* 4.0 13.3 - - + +
303B ALA* 1.3 78.7 - - - +
305B LYS* 1.3 82.0 + - + +
307B PHE* 3.1 24.5 - - - -
308B LEU* 4.8 0.2 - - - +
339C ARG* 5.2 5.7 + - - +
345C GLY* 5.3 1.6 - - - -
377C MET* 4.5 11.1 - - - -
380C LEU* 3.2 49.2 - - - +
381C ILE* 4.0 28.5 - - + +
384C GLU* 3.6 21.6 - - - +
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Residues in contact with LYS 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ILE* 3.5 21.8 - - + -
302B PRO* 3.1 16.6 + - + +
303B ALA 3.0 0.8 - - - -
304B GLU* 1.3 102.0 - - + +
306B VAL* 1.3 64.6 + - - +
307B PHE 3.3 2.2 - - - -
308B LEU* 3.1 20.3 + - + +
309B ALA* 3.1 10.0 + - - +
35C ILE* 3.2 46.1 + - + +
37C SER 4.5 8.3 + - - -
38C PRO* 5.4 0.8 - - - +
39C PRO* 4.9 2.4 - - - +
384C GLU* 2.5 36.8 + - - +
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Residues in contact with VAL 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ARG* 4.3 11.4 - - + +
297B LEU* 4.2 26.2 - - + +
298B GLY* 3.9 10.5 - - - +
301B ILE* 3.8 22.0 - - + +
302B PRO 3.3 18.2 - - - +
303B ALA* 3.6 3.9 + - - +
305B LYS* 1.3 76.5 - - - +
307B PHE* 1.3 58.3 + - - +
309B ALA* 3.1 6.2 + - - +
310B GLN* 2.8 29.3 + - + +
342C ARG* 3.7 40.6 - - + -
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Residues in contact with PHE 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ALA 4.5 3.9 + - - -
304B GLU* 3.1 32.8 - - - -
306B VAL* 1.3 78.8 - - - +
308B LEU* 1.3 86.4 + - + +
310B GLN* 3.7 9.2 - - - +
311B LYS* 3.1 47.5 + - + +
345C GLY 4.3 7.0 - - - -
346C SER* 3.5 29.0 + - - +
349C ALA* 3.5 32.8 - - + -
350C ASN* 5.6 3.4 - - - +
353C LEU* 4.4 11.4 - - + -
381C ILE* 4.8 3.8 - - + -
384C GLU* 4.1 3.1 - - + -
385C ALA* 3.7 27.6 - - + -
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Residues in contact with LEU 308 (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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304B GLU 4.8 1.8 - - - +
305B LYS* 3.1 14.9 + - + +
307B PHE* 1.3 110.4 - - + +
309B ALA* 1.3 59.5 + - - +
311B LYS* 3.3 4.2 + - + +
312B MET* 2.8 31.7 + - - +
33C LEU* 3.7 39.0 - - + +
34C ASP 5.1 10.3 - - - +
35C ILE* 4.2 10.5 - - + +
384C GLU* 3.2 42.6 - - + +
387C ALA* 5.2 4.7 - - + -
388C ALA* 4.3 7.0 - - + -
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Residues in contact with ALA 309 (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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277B VAL* 4.6 17.0 - - + -
297B LEU* 4.9 6.1 - - + -
301B ILE* 5.6 2.0 - - + -
305B LYS 3.1 12.3 + - - +
306B VAL* 3.6 11.0 - - - +
308B LEU* 1.3 74.9 - - - +
310B GLN* 1.3 57.6 + - - +
312B MET* 3.4 8.9 + - - +
313B MET* 2.9 48.3 + - + +
35C ILE* 3.9 20.1 - - + +
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Residues in contact with GLN 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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292B VAL* 4.4 11.9 - - + -
294B ARG* 2.9 43.3 + - + +
297B LEU* 5.6 0.2 - - - +
306B VAL* 2.8 17.9 + - + +
307B PHE* 3.7 10.3 - - - +
309B ALA* 1.3 77.9 - - - +
311B LYS* 1.3 57.7 + - - +
313B MET* 3.9 10.2 - - - +
314B ILE* 3.0 48.5 + - + +
326B CYS* 4.1 10.1 - - - -
347B ASP 5.4 0.6 + - - -
350B ASN* 5.9 0.4 - - - +
351B ALA* 3.8 20.8 - - - +
354B ASP* 3.2 21.4 + - - +
342C ARG* 4.8 2.9 + - - -
346C SER* 5.6 0.3 + - - -
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Residues in contact with LYS 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B PHE* 3.1 31.8 + - + +
308B LEU 3.7 4.3 - - - +
310B GLN* 1.3 77.1 - - - +
312B MET* 1.3 58.6 + - - +
314B ILE* 4.1 4.5 - - - +
315B GLY* 3.0 25.8 + - - -
350B ASN* 5.7 0.2 - - - +
354B ASP* 3.0 39.0 + - - +
26C PHE* 6.0 0.2 - - - -
30C MET* 3.6 38.1 - - + +
33C LEU* 3.8 14.4 - - + -
350C ASN* 3.1 25.1 + - - +
353C LEU* 3.5 27.1 - - + +
388C ALA* 4.7 3.8 - - + -
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Residues in contact with MET 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B VAL* 3.9 32.1 - - + +
280B PHE* 4.3 3.1 - - + -
308B LEU 2.8 17.4 + - - +
309B ALA* 3.7 7.4 - - - +
311B LYS* 1.3 76.4 - - - +
313B MET* 1.3 79.0 + - + +
315B GLY* 3.2 2.1 + - - -
316B ARG* 3.0 72.5 + - - +
30C MET 3.3 15.5 + - - +
31C CYS 3.7 5.8 - - - +
33C LEU* 3.2 28.0 - - + +
34C ASP* 6.1 0.7 - - - -
35C ILE* 6.0 2.5 - - + +
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Residues in contact with MET 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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271B ILE* 3.9 24.5 - - + -
277B VAL* 4.7 7.0 - - + -
280B PHE* 3.6 42.8 - - + -
290B ILE* 5.2 0.4 - - + -
292B VAL* 3.7 39.9 - - + -
297B LEU* 3.8 17.7 - - + -
309B ALA* 2.9 33.2 + - + +
310B GLN 4.0 1.8 - - - +
312B MET* 1.3 88.8 - - + +
314B ILE* 1.3 65.3 + - - +
316B ARG 3.4 0.3 + - - -
317B CYS* 3.0 30.9 + - - -
324B VAL* 4.9 0.7 - - - -
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Residues in contact with ILE 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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292B VAL* 4.7 2.9 - - + -
310B GLN* 3.0 30.5 + - + +
311B LYS* 4.1 3.4 - - - +
313B MET* 1.3 74.8 - - - +
315B GLY* 1.3 57.6 + - - +
317B CYS* 3.3 1.4 + - - +
318B ASN* 3.0 30.5 + - - +
324B VAL* 4.0 27.6 - - + -
326B CYS* 3.7 27.8 - - - -
351B ALA 4.1 5.2 - - - +
354B ASP* 3.3 45.1 - - + +
355B GLY 3.5 21.3 - - - +
356B ALA* 3.7 2.7 - - + +
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Residues in contact with GLY 315 (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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311B LYS 3.0 15.7 + - - -
312B MET 3.6 3.8 - - - -
313B MET 3.2 0.2 - - - -
314B ILE* 1.3 79.3 - - - +
316B ARG* 1.3 55.9 + - - +
318B ASN* 3.4 3.7 + - - -
319B ARG 3.0 22.7 + - - -
354B ASP 5.3 1.3 + - - -
27C LEU* 3.5 20.5 - - - +
30C MET* 4.6 6.7 - - - -
31C CYS* 3.5 16.7 - - - -
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Residues in contact with ARG 316 (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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277B VAL 5.3 1.6 + - - -
280B PHE* 3.7 25.0 - - + +
281B ASP* 3.1 37.0 + - - -
284B LEU* 3.6 8.7 - - + +
312B MET* 3.0 48.2 + - - +
313B MET 3.4 0.2 + - - -
315B GLY* 1.3 73.7 - - - +
317B CYS* 1.3 59.2 + - - +
319B ARG* 3.6 17.5 + - - +
320B ALA* 3.1 28.9 + - - +
31C CYS* 2.8 45.5 + - + +
32C ARG* 4.8 2.6 - - - +
33C LEU 4.1 6.1 + - - -
34C ASP* 5.3 5.3 + - - +
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Residues in contact with CYS 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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280B PHE* 3.9 4.9 - - - -
284B LEU* 3.9 14.6 - - - -
290B ILE* 3.7 37.7 - - - -
313B MET 3.0 24.6 + - - +
314B ILE 3.6 4.7 - - - +
315B GLY 3.2 0.2 - - - -
316B ARG* 1.3 76.1 - - - +
318B ASN* 1.3 59.4 + - - +
320B ALA* 3.3 1.6 + - - -
321B GLY 2.9 23.7 + - - -
322B LYS 2.9 28.2 + - - +
323B PRO 4.4 1.3 - - - -
324B VAL* 3.7 21.1 - - + -
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Residues in contact with ASN 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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314B ILE* 3.0 29.3 + - - +
315B GLY* 3.4 6.4 + - - +
317B CYS* 1.3 76.6 - - - +
319B ARG* 1.3 63.1 + - - +
321B GLY* 3.3 12.2 + - - +
322B LYS 5.0 0.6 + - - -
324B VAL* 4.2 2.6 - - - +
354B ASP 4.0 2.8 - - - +
355B GLY* 3.1 26.2 + - - +
357B ASP* 4.0 7.1 + - - -
398B LEU* 3.6 19.5 - - + +
443B ARG* 4.0 7.7 - - - +
445B ARG* 3.0 34.5 - - + +
27C LEU* 4.4 12.2 - - + +
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Residues in contact with ARG 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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281B ASP* 5.7 1.0 + - - -
315B GLY 3.0 17.8 + - - +
316B ARG* 3.8 21.1 - - - +
318B ASN* 1.3 76.4 - - - +
320B ALA* 1.3 53.6 + - - +
398B LEU* 4.2 11.2 - - + +
401B LEU* 5.1 17.3 - - + +
443B ARG* 2.4 36.5 + - - +
27C LEU* 4.1 13.8 - - + +
28C GLU* 4.8 8.9 - - - +
31C CYS* 3.3 35.7 - - - +
32C ARG* 4.4 16.8 - - - +
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Residues in contact with ALA 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B LEU* 4.0 20.2 - - + -
316B ARG 3.1 19.5 + - - +
317B CYS* 3.9 3.4 - - - +
319B ARG* 1.3 78.6 - - + +
321B GLY* 1.3 61.2 + - - +
322B LYS* 3.6 16.6 + - + +
443B ARG* 3.2 15.2 + - - +
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Residues in contact with GLY 321 (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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317B CYS 2.9 5.6 + - - -
318B ASN* 3.3 7.5 + - - -
319B ARG 3.3 0.4 - - - -
320B ALA* 1.3 80.0 - - - +
322B LYS* 1.3 61.7 + - - +
439B HIS* 5.1 3.1 - - - +
443B ARG* 3.6 33.9 - - - +
466B TYR* 4.0 18.9 + - - -
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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