Contacts of the helix formed by residues 300 - 318 (chain C) in PDB entry 3FAA
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 GLU 300 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298C THR* 2.7 18.5 + - + +
299C VAL* 1.3 75.3 - - - +
301C GLY* 1.3 66.7 + - - +
302C MET 3.2 0.4 - - - -
303C ILE* 3.3 19.6 + - + +
304C LYS* 3.9 20.4 + - - +
496C SER* 3.3 22.5 + - - -
499C GLU* 4.9 17.4 - - + +
500C GLY 4.2 10.2 - - - +
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Residues in contact with GLY 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C VAL* 3.2 15.6 - - - +
298C THR* 2.5 19.4 + - - +
300C GLU* 1.3 73.3 + - - +
302C MET* 1.3 54.3 + - - -
303C ILE 3.0 5.8 - - - -
304C LYS* 3.4 17.6 + - - +
305C LEU* 3.0 32.1 + - - +
345C GLY* 5.8 0.7 - - - -
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Residues in contact with MET 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C VAL* 3.2 19.4 - - + +
298C THR 2.7 8.1 + - - +
299C VAL* 3.9 10.3 - - + +
300C GLU 3.2 0.2 - - - -
301C GLY* 1.3 78.1 - - - +
303C ILE* 1.3 62.6 + - + +
305C LEU* 4.1 5.4 - - - +
306C ALA* 3.4 22.0 + - - +
411C ILE* 3.2 21.1 - - + -
412C ALA* 3.5 20.4 - - + -
415C CYS* 3.5 29.4 - - + -
463C ALA* 4.2 20.6 - - + -
464C LEU* 4.6 4.9 - - - +
467C MET* 3.4 41.1 - - + +
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Residues in contact with ILE 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C VAL 3.3 20.2 - - - +
300C GLU* 3.4 17.5 - - + +
301C GLY 3.0 0.8 - - - -
302C MET* 1.3 81.6 - - + +
304C LYS* 1.3 55.4 + - + +
306C ALA* 3.5 2.1 + - - +
307C LEU* 2.7 39.6 + - + +
463C ALA* 4.8 9.4 - - + -
467C MET* 6.2 1.1 - - + -
492C LEU* 4.1 20.1 - - + +
495C LEU* 3.4 36.8 - - + +
496C SER* 3.2 34.1 - - - +
499C GLU* 5.5 5.6 - - + +
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Residues in contact with LYS 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C GLU* 3.9 21.5 + - - +
301C GLY* 3.4 22.1 + - - -
303C ILE* 1.3 74.2 - - + +
305C LEU* 1.3 58.0 + - - +
306C ALA 2.8 11.2 + - - -
307C LEU* 3.8 12.3 - - + -
308C SER* 2.8 28.1 + - - -
344C ASN 4.3 4.2 + - - +
345C GLY* 3.8 27.2 - - - +
346C THR* 4.7 18.2 - - + +
496C SER* 5.2 2.2 - - - +
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Residues in contact with LEU 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C LEU* 3.7 30.5 - - + -
291C TYR* 3.8 24.9 - - + +
292C LEU* 5.1 4.7 - - + -
297C VAL* 5.0 5.2 - - + -
301C GLY 3.0 21.1 + - - +
302C MET* 4.1 6.3 - - - +
304C LYS* 1.3 77.2 - - - +
306C ALA* 1.3 56.2 + - - +
308C SER* 3.8 1.1 - - - -
309C THR* 3.2 15.1 + - - -
341C VAL* 3.5 33.7 - - + -
345C GLY* 3.7 9.7 + - - +
347C CYS* 3.4 17.2 - - - -
411C ILE* 3.9 20.3 - - + +
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Residues in contact with ALA 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C MET 3.4 17.5 + - - +
303C ILE 3.6 1.8 - - - +
304C LYS 2.9 0.2 - - - -
305C LEU* 1.3 80.8 - - - +
307C LEU* 1.3 61.5 + - - +
308C SER 3.3 1.6 - - - -
309C THR* 3.8 10.9 - - - -
310C ALA* 3.6 16.8 + - - +
408C PHE* 4.0 15.6 - - + -
411C ILE* 3.6 22.9 - - + -
467C MET* 4.3 14.1 - - + -
492C LEU* 3.9 10.7 - - + +
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Residues in contact with LEU 307 (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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303C ILE* 2.7 27.4 + - + +
304C LYS* 2.9 12.1 + - + +
306C ALA* 1.3 76.0 - - - +
308C SER* 1.3 56.5 + - - +
310C ALA* 3.2 6.4 + - + +
311C SER* 2.5 45.8 + - - +
488C ILE 6.0 0.2 - - - +
489C LYS* 5.2 7.0 - - + -
492C LEU* 3.8 20.2 - - + +
493C SER* 3.8 35.7 - - - +
496C SER* 4.7 4.7 - - - +
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Residues in contact with SER 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C ASN* 2.9 30.4 - - - -
304C LYS 2.8 16.4 + - - -
305C LEU 3.5 4.0 + - - -
307C LEU* 1.3 75.1 - - - +
309C THR* 1.3 61.0 + - - +
310C ALA 2.5 16.5 + - - -
311C SER* 2.7 4.5 + - - -
312C GLY* 2.6 28.1 + - - -
346C THR* 4.2 7.0 - - - -
347C CYS* 2.9 36.1 + - - +
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Residues in contact with THR 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C LEU* 4.8 3.6 - - - +
305C LEU 3.2 18.0 + - - -
306C ALA* 3.8 12.8 + - - -
308C SER* 1.3 82.5 + - - +
310C ALA* 1.3 56.6 + - - +
313C LEU* 3.2 19.9 + - - +
334C LEU* 4.6 8.3 - - + -
339C ILE* 3.9 35.9 - - + +
347C CYS* 4.3 2.0 - - - +
348C CYS* 6.1 0.7 - - - +
349C ILE* 3.8 10.6 - - + +
404C MET* 3.0 29.7 - - + +
407C VAL* 5.5 5.8 - - + -
408C PHE* 4.5 9.9 - - + -
411C ILE* 5.2 1.2 - - - +
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Residues in contact with ALA 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C ALA 3.6 9.8 + - - +
307C LEU* 3.2 9.1 + - - +
308C SER 2.5 4.6 + - - -
309C THR* 1.3 74.4 - - - +
311C SER* 1.3 64.0 + - - +
312C GLY 2.8 5.9 + - - -
313C LEU* 4.6 0.9 - - - -
314C ALA* 2.8 28.0 + - - +
404C MET* 3.4 17.0 - - + -
485C ALA* 5.3 4.1 - - - +
488C ILE* 4.4 22.0 - - + +
489C LYS* 4.4 15.7 - - + +
492C LEU* 5.0 0.4 - - + -
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Residues in contact with SER 311 (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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256C HIS* 3.6 18.1 + - - -
258C ASN* 3.7 16.9 + - - -
307C LEU* 2.5 34.8 + - - +
308C SER* 2.7 6.7 + - - -
310C ALA* 1.3 71.4 - - - +
312C GLY* 1.3 58.8 + - - +
314C ALA* 3.7 9.0 - - - +
315C HIS* 3.7 5.2 + - - +
489C LYS* 3.3 33.2 + - - +
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Residues in contact with GLY 312 (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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256C HIS* 4.1 5.6 - - - -
258C ASN* 3.6 25.5 - - - +
259C ILE* 5.0 2.8 - - - +
308C SER 2.6 17.6 + - - -
310C ALA 2.8 0.2 + - - -
311C SER* 1.3 71.0 - - - +
313C LEU* 1.3 51.6 + - - -
314C ALA 2.7 5.5 + - - -
315C HIS* 2.5 29.2 + - - +
316C LEU* 2.9 8.8 + - - +
349C ILE* 4.1 8.1 - - - -
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Residues in contact with LEU 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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309C THR 3.2 19.4 + - - +
310C ALA 3.3 2.8 + - - +
312C GLY* 1.3 72.2 - - - +
314C ALA* 1.3 60.3 + - - +
316C LEU* 3.6 27.1 - - + -
317C HIS* 3.2 54.4 + - + +
331C HIS* 4.3 5.4 - - + -
334C LEU* 3.2 35.4 - - + -
349C ILE* 3.8 11.4 - - + +
400C ASP* 4.5 6.3 - - + -
401C ILE* 4.6 8.1 - - + -
404C MET* 3.8 26.5 - - + -
485C ALA* 4.1 5.4 - - + +
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Residues in contact with ALA 314 (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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310C ALA 2.8 19.5 + - - +
311C SER 3.7 7.6 - - - +
312C GLY 2.7 0.8 + - - -
313C LEU* 1.3 77.9 - - - +
315C HIS* 1.3 52.0 + - - +
317C HIS* 3.3 2.1 + - - +
318C MET* 2.6 38.0 + - - +
485C ALA* 4.1 12.5 - - - +
486C LEU* 4.4 19.4 - - + +
489C LYS* 4.3 22.0 - - + +
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Residues in contact with HIS 315 (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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253C MET* 3.4 27.2 + - + +
254C LEU* 3.9 10.4 - - - +
255C ARG 4.1 2.8 + - - -
256C HIS* 3.6 30.7 - + + +
259C ILE* 3.7 18.6 - - + +
311C SER 3.7 8.7 + - - +
312C GLY 2.5 17.2 + - - +
314C ALA* 1.3 74.0 - - - +
316C LEU* 1.3 58.1 + - - +
318C MET* 3.3 19.7 - - + +
326C LYS* 3.0 38.0 + - + -
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Residues in contact with LEU 316 (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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254C LEU* 4.8 11.4 - - + -
259C ILE* 5.2 6.4 - - + +
312C GLY 2.9 5.9 + - - +
313C LEU* 3.6 28.0 - - + +
315C HIS* 1.3 79.5 + - - +
317C HIS* 1.3 58.0 + - + +
326C LYS* 3.1 14.0 + - - +
329C ILE* 2.9 66.5 + - + +
331C HIS* 3.7 39.7 - - + +
349C ILE* 4.0 12.8 - - + -
352C LEU* 4.5 18.2 - - + -
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Residues in contact with HIS 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C LEU* 3.2 47.2 + - + +
314C ALA 4.0 1.8 - - - +
316C LEU* 1.3 76.2 - - - +
318C MET* 1.3 66.8 + - - +
319C GLU 2.9 5.0 + - - -
328C ALA* 3.4 7.3 - - - +
329C ILE 3.3 23.3 + - - +
330C ALA* 4.5 1.7 - - - -
331C HIS 4.4 0.8 + - - -
397C LYS* 3.2 78.3 + - + +
400C ASP* 3.8 17.6 + - + -
401C ILE* 4.4 4.6 - - + +
485C ALA* 4.0 14.6 - - + +
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Residues in contact with MET 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C ALA 2.6 24.9 + - - +
315C HIS* 3.3 16.8 - - + +
316C LEU 3.3 0.2 - - - -
317C HIS* 1.3 69.9 - - - +
319C GLU* 1.3 91.4 + - + +
320C ILE* 4.7 4.9 - - + +
326C LYS* 3.0 27.7 + - + +
486C LEU* 5.6 13.7 - - - -
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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
------------------------------------------------------------
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