Contacts of the helix formed by residues 303 - 320 (chain C) in PDB entry 3ER8
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 303 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C ARG* 3.0 43.2 + - - -
142C LEU* 5.5 0.2 - - - +
143C ASN* 4.9 6.8 + - - -
301C ASP* 2.5 16.4 + - - +
302C PRO* 1.3 84.4 - - + +
304C LYS* 1.3 63.8 + - - +
305C PHE 3.3 2.7 - - - -
306C ASN* 3.1 32.7 + - - +
307C ALA* 3.9 3.3 + - - +
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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
----------------------------------------------------------
294C ARG* 5.6 3.9 - - - +
297C ASP* 5.0 11.9 - - + +
298C LEU* 4.7 0.4 - - + -
301C ASP* 2.6 41.8 + - + +
303C GLU* 1.3 71.9 - - - +
305C PHE* 1.3 106.1 + - + +
306C ASN 3.6 0.2 + - - -
307C ALA* 4.0 13.2 + - - +
308C ARG* 4.2 16.1 + - - +
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Residues in contact with PHE 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C LEU* 3.4 25.6 - - + +
285C MET* 3.6 34.3 - - + -
288C MET* 3.2 33.4 - - + -
289C PHE* 3.9 11.0 - + - -
294C ARG* 4.6 10.3 - - - -
297C ASP* 5.1 3.8 - - + -
298C LEU* 3.3 28.0 - - + +
303C GLU 3.3 0.4 - - - -
304C LYS* 1.3 117.0 - - + +
306C ASN* 1.3 59.4 + - - +
307C ALA 3.1 2.5 - - - -
308C ARG* 3.8 9.9 - - + +
309C MET* 2.4 40.6 + - + +
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Residues in contact with ASN 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C GLU* 2.9 24.8 + - - +
138C ALA* 3.2 4.4 - - - +
139C ARG* 2.7 68.9 + - - +
142C LEU* 2.9 16.8 - - + +
303C GLU* 3.1 24.4 + - - +
305C PHE* 1.3 76.0 - - - +
307C ALA* 1.3 57.3 + - - +
310C ALA* 2.8 38.3 + - - +
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Residues in contact with ALA 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C VAL* 5.0 2.3 - - - +
135C GLU* 6.3 1.1 - - - -
195C ASN* 4.8 0.8 + - - +
197C ASN 5.9 0.2 - - - +
198C ILE* 3.2 3.9 - - + +
303C GLU 3.9 3.4 + - - +
304C LYS 4.1 7.6 - - - +
306C ASN* 1.3 81.6 - - - +
308C ARG* 1.3 82.4 + - - +
310C ALA* 4.4 1.1 - - - +
311C THR* 2.6 34.8 + - - -
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Residues in contact with ARG 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C SER* 4.5 14.6 + - - +
191C LEU* 3.6 19.0 - - + +
197C ASN 4.5 2.0 + - - -
198C ILE* 2.7 59.7 - - - +
199C ARG* 3.3 44.7 + - - +
285C MET* 5.3 8.3 - - + -
304C LYS* 4.2 19.1 - - - +
305C PHE* 3.2 15.8 + - + +
307C ALA* 1.3 97.5 - - - +
309C MET* 1.3 63.5 + - - +
311C THR* 3.2 13.0 + - - -
312C MET* 3.2 20.3 + - - +
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Residues in contact with MET 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C ALA* 3.9 7.9 - - + +
141C MET* 4.8 9.2 - - - +
142C LEU* 3.2 31.0 - - + -
145C MET* 4.5 8.3 - - + -
282C LEU* 4.8 9.6 - - + +
285C MET* 4.1 17.7 - - + -
286C ILE* 6.5 0.4 - - + -
289C PHE* 3.0 39.0 - - + -
305C PHE* 2.4 36.3 + - + +
308C ARG* 1.3 65.8 - - - +
310C ALA* 1.3 58.1 + - - +
312C MET* 3.4 13.0 + - - +
313C LEU* 3.0 41.1 + - + +
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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
----------------------------------------------------------
131C VAL* 4.1 8.5 - - + +
134C MET* 3.6 25.9 - - - +
135C GLU* 3.9 9.6 - - + +
138C ALA* 3.3 17.4 - - + +
306C ASN 2.8 24.3 + - - +
307C ALA* 4.4 1.1 - - - +
309C MET* 1.3 69.1 - - - +
311C THR* 1.3 56.0 + - - +
312C MET 2.7 16.1 + - - -
313C LEU* 3.8 4.9 - - - +
314C GLU* 2.9 28.0 + - - +
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Residues in contact with THR 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C VAL* 3.2 20.0 - - + +
191C LEU* 3.9 17.2 - - + +
194C ILE* 4.1 15.5 - - + +
195C ASN* 3.2 32.8 + - + -
198C ILE* 2.9 21.1 - - + +
307C ALA 2.6 22.8 + - - -
308C ARG* 3.2 7.8 + - - -
310C ALA* 1.3 78.5 - - - +
312C MET* 1.3 57.6 + - - +
314C GLU* 4.0 2.9 - - - +
315C TYR* 3.7 16.8 + - - +
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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
----------------------------------------------------------
191C LEU* 3.7 35.2 - - + -
278C PRO* 3.9 10.8 - - + +
281C GLN* 4.2 8.7 - - - +
282C LEU* 3.5 58.7 - - + +
285C MET* 3.6 34.1 - - + -
308C ARG* 3.2 17.9 + - + +
309C MET* 3.6 8.7 - - - +
310C ALA 2.7 1.6 + - - -
311C THR* 1.3 78.1 - - - +
313C LEU* 1.3 61.1 + - - +
314C GLU 2.9 6.1 - - - -
315C TYR* 3.0 17.2 + - - +
316C VAL* 3.1 11.1 + - - +
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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
----------------------------------------------------------
134C MET* 3.9 8.4 - - + +
137C LEU* 3.8 26.9 - - + -
138C ALA* 4.0 11.2 - - + +
141C MET* 3.7 28.3 - - - -
282C LEU* 4.0 11.0 - - + -
309C MET* 3.0 37.9 + - + +
310C ALA 3.0 1.1 + - - +
312C MET* 1.3 74.0 - - - +
314C GLU* 1.3 57.2 + - - +
316C VAL* 3.4 7.3 - - - +
317C ARG* 3.2 28.1 + - - +
324C PHE* 3.6 17.3 - - + -
443C LEU* 3.5 32.3 - - + -
446C MET* 4.8 0.9 - - + -
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Residues in contact with GLU 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ASN* 3.0 32.8 - - + +
131C VAL* 3.5 16.4 - - + +
133C SER* 2.9 20.3 + - - -
134C MET* 3.3 22.8 - - + +
310C ALA 2.9 17.3 + - - +
311C THR 4.0 5.4 - - - +
313C LEU* 1.3 78.7 - - - +
315C TYR* 1.3 61.2 + - - +
317C ARG* 2.7 35.4 + - - +
318C TYR* 3.6 17.5 + - - +
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Residues in contact with TYR 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C ILE* 4.2 25.1 - - + -
268C ILE* 3.6 31.4 - - + +
277C ASP* 4.5 1.2 + - - -
278C PRO* 3.7 39.9 - - + -
279C THR* 3.7 19.5 - - - -
311C THR 3.7 13.1 + - - +
312C MET* 3.0 11.5 + - - +
314C GLU* 1.3 78.0 - - - +
316C VAL* 1.3 62.3 + - - +
318C TYR* 3.4 3.0 + - - +
319C THR* 2.6 70.8 + - + +
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Residues in contact with VAL 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C THR* 4.3 14.4 - - + +
282C LEU* 4.2 11.7 - - + -
312C MET 3.1 10.2 + - - +
313C LEU* 3.4 16.8 - - - +
315C TYR* 1.3 84.2 - - + +
317C ARG* 1.3 78.7 + - - +
319C THR* 4.3 2.9 - - - -
320C HIS* 2.9 26.6 + - + -
322C ILE* 3.2 30.0 - - + +
324C PHE* 3.7 17.7 - - + -
439C LEU* 3.8 26.7 - - + -
443C LEU* 4.1 7.0 - - + -
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Residues in contact with ARG 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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133C SER* 4.9 4.2 + - - -
134C MET* 3.8 19.8 - - - -
313C LEU 3.2 17.6 + - - +
314C GLU* 2.7 35.3 + - - +
315C TYR 3.4 0.2 - - - -
316C VAL* 1.3 81.3 - - - +
318C TYR* 1.3 77.9 + - - +
321C GLY* 3.0 5.4 - - - -
322C ILE 2.9 31.8 + - - +
324C PHE* 3.4 20.4 - - + -
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Residues in contact with TYR 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 GLU* 3.6 11.7 + - - +
315C TYR* 3.4 6.2 + - - +
316C VAL 3.1 0.8 - - - -
317C ARG* 1.3 90.7 - - - +
319C THR* 1.3 63.4 + - - +
320C HIS 2.5 4.0 + - - -
321C GLY* 2.4 32.6 + - - -
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Residues in contact with THR 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C ASP* 5.8 0.9 - - - +
279C THR* 4.6 0.2 - - - +
315C TYR* 2.6 64.9 + - + +
316C VAL* 4.2 1.3 - - - -
318C TYR* 1.3 86.7 - - - +
320C HIS* 1.3 89.1 + - + +
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Residues in contact with HIS 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C ASP* 5.5 3.2 + - - -
279C THR* 4.2 20.5 + - + -
316C VAL* 2.9 14.0 + - + +
318C TYR 2.5 3.0 + - - -
319C THR* 1.3 101.4 + - + +
321C GLY* 1.3 68.3 + - - +
322C ILE* 2.8 21.4 + - + +
435C TYR* 3.7 15.7 + + - -
436C LYS* 3.1 43.4 + - + +
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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