Contacts of the helix formed by residues 305 - 321 (chain C) in PDB entry 3G2G
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 LYS 305 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C ILE* 4.2 7.0 - - + -
302C PRO* 2.9 36.1 + - + +
304C GLU* 1.3 83.6 - - + +
306C VAL* 1.3 64.4 + - - +
307C PHE 3.2 2.9 - - - -
308C LEU* 3.0 31.9 + - + +
309C ALA 3.3 4.2 + - - -
35D ILE* 3.2 42.1 + - + +
36D ASP 5.5 0.4 - - - -
37D SER 4.4 6.3 + - - -
38D PRO* 4.6 4.8 - - - +
39D PRO* 4.3 10.1 - - - +
384D GLU* 2.6 41.2 + - - +
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Residues in contact with VAL 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C VAL* 5.5 0.2 - - + -
294C ARG* 4.0 38.4 - - + +
297C LEU* 4.4 11.4 - - + -
298C GLY* 3.4 34.3 - - - +
301C ILE* 4.4 9.9 - - + -
302C PRO 4.2 2.9 - - - +
303C ALA* 3.4 21.6 + - - +
305C LYS* 1.3 78.2 - - - +
307C PHE* 1.3 58.3 + - - +
309C ALA* 3.1 4.7 + - - +
310C GLN* 2.8 27.7 + - + +
342D ARG* 4.7 10.1 - - + +
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Residues in contact with PHE 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C ALA 4.9 0.8 + - - -
304C GLU 3.1 28.3 - - - -
305C LYS 3.2 0.2 + - - -
306C VAL* 1.3 79.3 - - - +
308C LEU* 1.3 86.7 + - + +
310C GLN* 3.7 10.0 - - - +
311C LYS* 3.0 56.5 + - + +
33D LEU* 5.8 0.2 - - + -
345D GLY 5.1 2.7 - - - +
346D SER* 4.7 15.5 - - - +
349D ALA* 3.4 32.1 - - + -
350D ASN* 5.7 0.7 - - - +
353D LEU* 4.4 6.1 - - + -
381D ILE* 4.5 5.4 - - + -
384D GLU* 3.7 10.8 - - + -
385D ALA* 3.5 33.9 - - + -
388D ALA* 4.1 9.2 - - + -
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Residues in contact with LEU 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C LYS* 3.0 29.4 + - + +
307C PHE* 1.3 106.8 - - + +
309C ALA* 1.3 59.3 - - - +
311C LYS* 3.3 1.4 + - - +
312C MET* 2.8 33.2 + - - +
17D GLN* 3.7 28.0 - - - +
33D LEU* 4.1 19.5 - - + +
35D ILE* 4.1 17.7 - - + +
384D GLU* 3.7 25.6 - - - +
388D ALA* 3.8 16.4 - - + -
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Residues in contact with ALA 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C VAL* 4.4 9.2 - - + -
297C LEU* 3.9 14.4 - - + -
301C ILE* 4.6 2.0 - - + -
305C LYS 3.3 3.6 + - - +
306C VAL* 3.1 9.5 + - - +
308C LEU* 1.3 77.7 - - - +
310C GLN* 1.3 57.2 + - - +
312C MET* 3.8 8.8 - - - +
313C MET* 2.9 55.1 + - + +
35D ILE* 3.8 20.7 - - + +
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Residues in contact with GLN 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C VAL* 3.9 23.5 - - + +
294C ARG* 2.9 37.6 + - - +
306C VAL* 2.8 17.8 + - - +
307C PHE* 3.7 11.0 - - - +
309C ALA* 1.3 76.3 - - - +
311C LYS* 1.3 59.9 + - - +
313C MET* 3.3 2.3 + - - +
314C ILE* 2.9 43.6 + - + +
326C CYS* 3.8 19.0 - - - -
347C ASP* 5.0 2.4 + - - -
350C ASN* 5.9 0.4 - - - +
351C ALA* 4.1 12.5 - - - +
354C ASP* 3.0 22.9 + - - +
346D SER* 5.0 6.7 + - - -
350D ASN* 5.9 1.0 - - - +
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Residues in contact with LYS 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C PHE* 3.0 36.4 + - + +
310C GLN* 1.3 76.3 - - + +
312C MET* 1.3 65.8 + - - +
314C ILE* 4.7 1.8 - - - -
315C GLY* 3.0 20.4 + - - -
350C ASN* 5.0 0.4 + - - -
354C ASP* 2.8 42.8 + - - +
26D PHE* 6.6 0.2 - - + -
30D MET* 3.3 27.8 - - + +
33D LEU* 4.0 22.9 - - + -
350D ASN* 2.8 35.6 + - - +
353D LEU* 3.5 23.9 - - + +
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Residues in contact with MET 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C VAL* 3.8 29.6 - - + +
280C PHE* 4.2 14.8 - - + -
308C LEU 2.8 18.5 + - - +
309C ALA* 3.8 5.4 - - - +
311C LYS* 1.3 78.3 - - - +
313C MET* 1.3 80.0 + - + +
315C GLY* 3.8 0.5 - - - -
316C ARG* 2.9 64.6 + - - +
30D MET 3.2 12.5 + - - +
31D CYS* 3.2 22.7 - - - +
33D LEU* 3.4 20.4 - - - +
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Residues in contact with MET 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271C ILE* 3.7 38.1 - - + -
277C VAL* 4.3 4.0 - - + -
280C PHE* 3.3 37.4 - - + -
290C ILE* 4.3 7.6 - - + -
292C VAL* 4.0 23.8 - - + -
297C LEU* 3.9 13.5 - - + -
309C ALA* 2.9 45.4 + - + +
310C GLN 3.9 2.5 - - - +
312C MET* 1.3 87.4 - - + +
314C ILE* 1.3 58.6 + - - +
316C ARG* 3.3 1.4 + - - +
317C CYS* 2.9 35.9 + - - -
324C VAL* 4.6 0.7 - - - -
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Residues in contact with ILE 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C VAL* 4.4 4.3 - - + -
310C GLN* 2.9 40.0 + - + +
311C LYS 4.2 2.0 - - - +
313C MET* 1.3 74.6 - - - +
315C GLY* 1.3 57.6 + - - +
317C CYS* 3.2 0.9 + - - +
318C ASN* 2.8 30.7 + - - +
324C VAL* 3.9 26.7 - - + -
326C CYS* 4.8 5.8 - - + -
351C ALA 4.2 0.7 - - - +
354C ASP* 3.3 47.1 - - + +
355C GLY* 3.4 23.1 - - - +
356C ALA* 3.9 19.5 - - + -
30D MET* 4.6 0.2 - - + -
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Residues in contact with GLY 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C LYS 3.0 17.7 + - - -
312C MET 3.8 1.1 - - - -
314C ILE* 1.3 78.9 - - - +
316C ARG* 1.3 54.9 + - - +
318C ASN* 3.4 4.3 + - - +
319C ARG* 2.9 27.9 + - - +
27D LEU* 3.6 20.7 - - - +
30D MET* 4.0 10.7 - - - +
31D CYS* 3.3 12.9 - - - -
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Residues in contact with ARG 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C VAL 5.5 0.8 + - - -
280C PHE* 3.8 24.2 - - + +
281C ASP* 3.0 34.4 + - - -
284C LEU* 3.7 7.6 - - + +
312C MET* 2.9 46.2 + - - +
315C GLY* 1.3 73.7 - - - +
317C CYS* 1.3 61.2 + - - +
319C ARG* 3.5 31.8 + - - +
320C ALA* 3.0 28.4 + - - +
31D CYS* 2.9 37.1 + - + -
32D ARG* 4.8 4.2 - - - +
33D LEU 5.0 2.0 + - - -
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Residues in contact with CYS 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C PHE* 4.0 5.4 - - - -
284C LEU* 3.9 15.7 - - - -
290C ILE* 3.6 38.1 - - - -
313C MET 2.9 24.3 + - - +
314C ILE 3.7 2.0 - - - +
316C ARG* 1.3 74.6 - - - +
318C ASN* 1.3 59.8 + - - +
320C ALA* 3.1 1.9 + - - -
321C GLY 2.8 25.5 + - - -
322C LYS 3.1 27.8 + - - +
323C PRO 4.4 1.1 - - - -
324C VAL* 3.6 21.3 - - + -
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Residues in contact with ASN 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314C ILE* 2.8 23.9 + - - +
315C GLY* 3.5 5.1 - - - +
317C CYS* 1.3 71.4 - - - +
319C ARG* 1.3 63.9 + - - +
321C GLY* 3.2 11.7 + - - -
322C LYS 5.2 0.4 + - - -
324C VAL* 4.5 1.8 - - - +
354C ASP 3.7 6.9 - - - +
355C GLY* 3.1 40.6 + - - -
357C ASP* 4.4 4.2 + - - -
394C LEU* 5.2 9.1 - - + +
398C LEU* 4.1 18.9 - - + +
443C ARG* 3.6 10.9 + - - +
445C ARG* 3.2 25.1 + - + +
27D LEU* 4.4 13.8 - - + +
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Residues in contact with ARG 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281C ASP* 4.8 6.9 + - - -
315C GLY 2.9 16.6 + - - +
316C ARG* 3.5 38.4 + - - +
317C CYS 3.2 0.2 - - - -
318C ASN* 1.3 75.6 - - - +
320C ALA* 1.3 53.9 + - - +
398C LEU* 5.0 2.5 - - - -
401C LEU* 5.0 27.3 - - + +
443C ARG* 2.4 24.9 + - - +
27D LEU* 4.8 10.0 - - + +
28D GLU* 2.6 43.7 + - - -
31D CYS* 3.8 16.2 - - - +
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Residues in contact with ALA 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C LEU* 3.8 22.4 - - + -
316C ARG 3.0 18.0 + - - +
317C CYS 3.8 3.1 - - - +
319C ARG* 1.3 76.7 - - - +
321C GLY* 1.3 63.2 + - - +
322C LYS* 4.3 15.5 - - + +
443C ARG* 3.5 12.5 + - - +
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Residues in contact with GLY 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317C CYS 2.8 10.1 + - - -
318C ASN* 3.2 10.6 + - - -
319C ARG 3.3 0.4 - - - -
320C ALA* 1.3 74.6 - - - +
322C LYS* 1.3 62.2 + - - +
323C PRO* 4.4 2.8 - - - +
439C HIS* 5.6 2.4 - - - +
443C ARG* 3.5 34.5 - - - +
466C TYR* 4.7 9.6 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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