Contacts of the helix formed by residues 307 - 326 (chain C) in PDB entry 3K6G
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 SER 307 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306C VAL* 1.3 75.9 - - - +
308C GLN* 1.3 64.6 + - - +
309C PRO* 3.5 17.1 - - - +
310C GLU* 2.8 47.4 + - - +
311C VAL* 3.2 20.1 + - - +
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Residues in contact with GLN 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C VAL 3.8 1.0 + - - -
307C SER* 1.3 71.1 - - - +
309C PRO* 1.3 66.3 - - + +
311C VAL* 3.2 10.9 + - + +
312C GLY* 2.9 25.3 + - - -
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Residues in contact with PRO 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C SER* 3.3 17.3 - - - +
308C GLN* 1.3 95.6 - - + +
310C GLU* 1.3 59.8 + - + +
312C GLY* 3.4 2.0 + - - +
313C ALA* 3.0 26.9 + - - +
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Residues in contact with GLU 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C VAL* 5.3 1.2 - - - -
307C SER* 2.8 36.8 + - - +
308C GLN 3.2 0.6 - - - -
309C PRO* 1.3 77.6 - - + +
311C VAL* 1.3 61.5 + - - +
313C ALA* 3.2 7.3 + - - +
314C ALA* 2.8 29.1 + - - +
287F THR* 3.8 26.1 + - + +
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Residues in contact with VAL 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C VAL* 3.4 23.3 - - + +
307C SER 3.2 17.7 - - - +
308C GLN* 3.2 12.3 + - + +
310C GLU* 1.3 73.1 - - - +
312C GLY* 1.3 61.2 + - - +
314C ALA* 3.2 1.8 + - - +
315C ILE* 2.8 45.9 + - + +
287F THR* 4.0 8.5 - - + -
290F ALA* 3.9 16.6 - - + +
291F ALA* 3.8 28.3 - - - +
294F THR* 4.5 4.7 - - - +
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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
----------------------------------------------------------
308C GLN 2.9 15.1 + - - -
309C PRO* 3.7 4.3 - - - -
311C VAL* 1.3 77.7 - - - +
313C ALA* 1.3 60.7 + - - +
315C ILE* 3.2 12.9 + - - +
316C LYS* 3.0 30.0 + - - +
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Residues in contact with ALA 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 PRO 3.0 14.4 + - - +
310C GLU* 3.5 11.0 - - - +
312C GLY* 1.3 74.9 - - - +
314C ALA* 1.3 63.1 + - - +
316C LYS* 3.1 10.9 + - - +
317C ILE* 2.9 37.7 + - + +
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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
----------------------------------------------------------
310C GLU 2.8 17.6 + - - +
311C VAL 3.5 4.9 - - - +
313C ALA* 1.3 75.9 - - - +
315C ILE* 1.3 56.6 + - - +
317C ILE* 3.2 10.8 + - - +
318C ILE* 2.8 38.0 + - + +
283F ILE* 4.1 19.3 - - + -
287F THR* 3.9 18.6 - - + -
291F ALA* 3.9 14.6 - - + -
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Residues in contact with ILE 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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311C VAL* 2.8 32.8 + - + +
312C GLY* 3.4 12.1 - - - +
314C ALA* 1.3 75.9 - - - +
316C LYS* 1.3 58.4 + - + +
318C ILE* 3.3 6.1 + - - +
319C ARG* 2.8 56.1 + - - +
291F ALA* 4.0 20.0 - - + +
294F THR* 3.8 29.6 - - + -
295F LEU* 3.9 19.5 - - + -
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Residues in contact with LYS 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C GLY 3.0 18.0 + - - +
313C ALA* 3.5 11.2 - - - +
315C ILE* 1.3 78.1 - - + +
317C ILE* 1.3 59.0 + - + +
319C ARG* 3.3 8.3 + - - +
320C GLN* 2.8 45.0 + - + +
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Residues in contact with ILE 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C ALA* 2.9 32.4 + - + +
314C ALA* 3.5 6.5 - - - +
316C LYS* 1.3 76.8 - - + +
318C ILE* 1.3 64.2 + - - +
320C GLN* 3.2 12.5 + - - +
321C LEU* 3.0 26.6 + - + +
336C PHE* 4.0 15.5 - - + -
343C LEU* 3.4 42.6 - - + -
281F THR* 5.1 5.8 - - + -
283F ILE* 4.1 20.6 - - + -
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Residues in contact with ILE 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C ALA* 2.8 25.8 + - + +
315C ILE* 3.8 5.4 - - - +
317C ILE* 1.3 72.5 - - - +
319C ARG* 1.3 60.6 + - - +
321C LEU* 3.4 2.8 + - - +
322C MSE 3.0 50.2 + - + +
329C LEU* 3.9 16.4 - - + -
332C VAL* 4.1 19.4 - - + +
333C THR* 4.7 9.2 - - - +
336C PHE* 4.1 19.3 - - + -
283F ILE* 4.9 2.0 - - + -
288F LEU* 3.8 26.7 - - + +
291F ALA* 3.8 22.9 - - + -
292F PHE 5.0 2.7 - - - +
295F LEU* 4.5 3.4 - - + -
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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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315C ILE* 2.8 51.1 + - + +
316C LYS* 3.7 8.3 - - - +
318C ILE* 1.3 74.7 - - - +
320C GLN* 1.3 63.1 + - + +
322C MSE 3.2 24.0 + - + +
323C GLU* 3.0 33.8 + - - +
295F LEU* 4.2 16.9 - - + +
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Residues in contact with GLN 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C LYS* 2.8 38.4 + - + +
317C ILE* 3.2 12.2 + - - +
319C ARG* 1.3 74.4 - - + +
321C LEU* 1.3 58.5 + - + +
323C GLU* 3.0 20.1 + - - +
324C LYS* 2.9 31.3 + - - +
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Residues in contact with LEU 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 ILE* 3.0 24.8 + - + +
318C ILE 3.8 3.8 - - - +
320C GLN* 1.3 73.7 - - + +
322C MSE 1.3 66.5 + - - +
324C LYS* 4.2 8.3 - - + -
325C PHE* 3.1 54.7 + - + +
332C VAL* 4.2 14.9 - - + +
336C PHE* 3.4 41.3 - - + -
343C LEU* 4.7 6.1 - - + -
346C THR* 4.8 3.8 - - + -
347C SER* 4.0 21.3 - - - +
350C LEU* 4.7 8.3 - - + -
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Residues in contact with MSE 322 (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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318C ILE* 3.0 42.5 + - + +
319C ARG* 3.2 41.0 + - + +
321C LEU* 1.3 76.3 - - - +
323C GLU* 1.3 57.9 + - - +
326C ASN* 2.8 26.5 + - - -
327C LEU 2.9 26.6 + - - +
328C ASP* 4.2 1.6 - - - +
329C LEU* 3.7 30.3 - - + -
332C VAL* 3.7 17.7 - - + +
295F LEU* 4.0 12.1 - - + -
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Residues in contact with GLU 323 (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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319C ARG* 3.0 26.0 + - - +
320C GLN* 3.0 29.8 + - - +
322C MSE 1.3 73.4 - - - +
324C LYS* 1.3 64.6 + - - +
325C PHE 3.5 0.3 + - - -
326C ASN* 3.6 10.1 + - - +
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Residues in contact with LYS 324 (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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320C GLN 2.9 19.5 + - - +
321C LEU* 3.8 12.1 - - + +
322C MSE 3.3 0.2 - - - -
323C GLU* 1.3 79.5 - - + +
325C PHE* 1.3 95.8 + - + +
326C ASN* 5.4 0.2 - - - +
347C SER* 4.7 7.6 - - - +
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Residues in contact with PHE 325 (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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321C LEU* 3.1 43.5 + - + +
324C LYS* 1.3 107.9 - - + +
326C ASN* 1.3 73.0 + - - +
327C LEU* 3.5 24.2 + - + +
347C SER* 3.6 20.4 - - - -
350C LEU* 3.9 30.3 - - + +
351C ALA* 3.7 26.5 - - + -
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Residues in contact with ASN 326 (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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322C MSE 2.8 12.8 + - - -
323C GLU* 3.6 7.0 + - - +
324C LYS 3.5 2.6 - - - +
325C PHE* 1.3 82.5 - - - +
327C LEU* 1.3 61.8 + - - +
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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
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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