Contacts of the helix formed by residues 305 - 318 (chain C) in PDB entry 3Q6N
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 THR 305 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303C ASP 4.1 2.5 + - - +
304C ILE* 1.3 76.3 - - - +
306C ASN* 1.3 66.3 + - - +
307C GLU* 4.2 10.9 + - - +
308C GLU* 3.0 40.7 + - - +
309C TYR* 3.5 8.2 + - - -
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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
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304C ILE 3.8 1.0 + - - -
305C THR* 1.3 72.6 - - - +
307C GLU* 1.3 64.1 + - - +
308C GLU 3.3 0.2 + - - -
309C TYR* 3.4 11.2 + - - +
310C GLY* 3.1 19.4 + - - -
322C ASP* 4.0 18.4 + - - -
323C HIS* 3.5 20.8 + - - -
326C VAL* 5.2 2.6 - - - +
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Residues in contact with GLU 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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305C THR* 3.1 10.7 + - - +
306C ASN* 1.3 79.6 - - - +
308C GLU* 1.3 66.3 + - - +
310C GLY* 3.5 2.0 + - - -
311C GLU* 3.1 38.7 + - + +
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Residues in contact with GLU 308 (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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298C THR* 5.5 3.3 + - - +
303C ASP 5.0 1.6 - - - +
304C ILE* 3.7 23.0 - - + +
305C THR* 3.0 27.8 + - - +
307C GLU* 1.3 86.1 - - - +
309C TYR* 1.3 65.3 + - - +
311C GLU* 3.2 13.8 + - - +
312C PHE* 3.0 24.1 + - - +
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Residues in contact with TYR 309 (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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298C THR* 5.3 3.8 - - - -
302C ASP* 3.8 10.4 + - - -
304C ILE* 3.7 40.1 - - + +
305C THR 3.5 12.3 + - - -
306C ASN* 3.4 14.1 + - - +
308C GLU* 1.3 75.8 - - - +
310C GLY* 1.3 57.4 + - - +
312C PHE* 3.3 7.1 + - + +
313C TYR* 2.9 29.5 + - - +
323C HIS* 3.8 15.9 - - + +
326C VAL* 4.1 29.2 - - + -
328C HIS* 2.7 34.1 + - + +
340C LEU* 3.7 29.4 - - + -
342C PHE* 3.6 12.4 - + + -
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Residues in contact with GLY 310 (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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306C ASN 3.1 9.9 + - - -
307C GLU* 3.8 4.0 - - - -
308C GLU 3.2 0.2 - - - -
309C TYR* 1.3 77.7 - - - +
311C GLU* 1.3 49.7 + - - +
313C TYR* 3.1 5.0 + - - +
314C LYS* 2.8 43.4 + - - +
322C ASP* 4.0 11.4 - - - -
323C HIS* 3.3 24.1 + - - -
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Residues in contact with GLU 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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307C GLU* 3.1 31.9 + - + +
308C GLU* 3.6 13.9 - - - +
310C GLY* 1.3 71.4 - - - +
312C PHE* 1.3 61.6 + - - +
314C LYS* 3.9 17.8 - - + +
315C SER* 3.0 25.5 + - - -
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Residues in contact with PHE 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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298C THR* 3.5 38.1 - - + +
299C ARG* 4.3 7.0 - - - -
308C GLU 3.0 12.7 + - - +
309C TYR* 3.5 9.2 - - - +
311C GLU* 1.3 74.8 - - - +
313C TYR* 1.3 63.9 + - - +
315C SER* 2.7 23.5 + - - -
316C LEU* 3.0 37.5 + - + +
340C LEU* 4.0 5.2 - - + -
342C PHE* 3.7 22.2 - + - -
388C VAL* 3.7 32.5 - - + -
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Residues in contact with TYR 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 TYR 2.9 14.0 + - - +
310C GLY 3.3 6.5 - - - +
312C PHE* 1.3 76.6 - - - +
314C LYS* 1.3 57.4 + - - +
316C LEU* 3.2 7.0 + - + +
317C THR* 2.4 61.8 + - + +
319C ASP* 2.9 30.2 + - + +
321C GLU 3.6 11.2 - - - -
322C ASP* 3.8 5.8 - - - -
323C HIS* 3.4 30.1 - - + -
342C PHE* 3.5 51.4 - + + -
344C PRO* 3.5 30.8 - - + +
386C ARG* 4.3 7.6 - - + +
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Residues in contact with LYS 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 GLY 2.8 24.0 + - - +
311C GLU* 3.9 16.5 - - + +
313C TYR* 1.3 74.4 - - - +
315C SER* 1.3 56.2 + - - +
317C THR* 3.1 6.3 + - - -
318C ASN* 2.8 36.0 + - - -
319C ASP 3.6 22.2 - - - +
320C TRP* 4.7 4.4 + - - -
321C GLU* 4.0 17.3 - - - +
322C ASP* 4.1 24.0 - - - +
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Residues in contact with SER 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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318B ASN* 5.2 8.3 + - - -
311C GLU 3.0 13.6 + - - -
312C PHE* 2.7 28.1 + - - -
314C LYS* 1.3 76.9 - - - +
316C LEU* 1.3 58.7 + - - +
318C ASN* 4.5 9.4 - - - +
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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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312C PHE* 3.0 48.3 + - + +
313C TYR* 3.5 4.9 - - - +
314C LYS 3.0 0.4 - - - -
315C SER* 1.3 79.5 - - - +
317C THR* 1.3 66.6 + - + +
318C ASN* 3.9 0.9 - - - -
342C PHE* 4.4 9.6 - - + -
360C ASN 5.2 4.7 - - - +
362C LYS* 3.7 45.9 + - + +
386C ARG 4.9 0.7 - - - -
387C GLY* 3.9 33.0 - - - +
388C VAL* 5.2 2.0 - - + -
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Residues in contact with THR 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C TYR* 2.4 51.5 + - + +
314C LYS 3.4 3.5 + - - -
316C LEU* 1.3 86.6 - - + +
318C ASN* 1.3 68.0 + - - +
319C ASP* 3.5 19.6 - - - +
386C ARG* 3.8 30.1 - - + +
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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 LYS 2.8 11.8 + - - +
315C SER* 4.6 9.2 - - - +
316C LEU 5.3 0.5 - - - -
317C THR* 1.3 79.7 + - - +
319C ASP* 1.3 61.0 + - - +
320C TRP* 3.8 3.5 + - - -
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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