Contacts of the helix formed by residues 306 - 319 (chain C) in PDB entry 3DEG
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 ASP 306 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C PRO* 4.0 10.3 - - + -
302C VAL* 5.5 0.2 - - - +
303C SER* 3.0 33.0 + - - +
305C ASP* 1.3 78.3 - - - +
307C TYR* 1.3 58.9 + - - +
308C GLU 3.2 1.6 - - - -
309C ALA* 3.0 10.7 + - - +
310C PHE* 2.8 28.9 + - - +
360C ASP 5.3 2.3 - - - +
361C LEU* 3.9 23.0 - - + +
362C ASP* 4.4 18.6 + - - +
363C LEU* 5.9 0.2 - - + -
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Residues in contact with TYR 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C PRO* 4.1 14.8 - - + +
304C SER* 3.2 20.4 + - - +
306C ASP* 1.3 76.9 - - - +
308C GLU* 1.3 75.1 + - + +
310C PHE* 3.3 2.3 + - - +
311C ARG* 3.0 54.1 + - - +
328C PRO* 4.9 0.2 - - - +
336C PHE* 3.3 45.7 - + + +
337C GLY* 4.2 2.2 - - - -
338C PHE* 3.5 34.9 - + - -
32D VAL* 4.7 9.9 - - + +
76D HIS* 3.3 23.6 + + - +
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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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304C SER 5.6 0.9 - - - +
305C ASP* 4.3 13.9 - - - +
306C ASP 3.2 0.6 - - - -
307C TYR* 1.3 88.6 - - + +
309C ALA* 1.3 63.9 + - - +
311C ARG* 3.3 29.9 + - - +
312C ASP* 3.1 32.6 + - - +
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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
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305C ASP 4.9 0.6 + - - +
306C ASP* 3.0 12.6 + - - +
308C GLU* 1.3 79.9 - - - +
310C PHE* 1.3 57.3 + - - +
312C ASP* 3.4 8.1 + - - +
313C ALA* 2.9 30.9 + - - +
359C TYR* 5.4 3.3 - - + +
361C LEU* 4.0 16.8 - - + -
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Residues in contact with PHE 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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299C LEU* 3.2 51.1 - - + -
301C PRO* 3.9 21.3 - - + -
306C ASP 2.8 16.2 + - - +
307C TYR* 3.6 6.7 - + - +
309C ALA* 1.3 74.5 - - - +
311C ARG* 1.3 63.4 + - - +
313C ALA* 3.3 0.7 + - - +
314C LEU* 3.0 44.0 + - + +
337C GLY* 4.9 0.2 - - - -
338C PHE* 3.6 23.8 - + + -
340C CYS* 5.2 0.2 - - - -
355C LEU* 3.9 17.3 - - + -
361C LEU* 3.8 25.7 - - + +
363C LEU* 3.8 21.5 - - + -
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Residues in contact with ARG 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C TYR* 3.0 41.9 + - + +
308C GLU* 3.4 26.8 + - - +
310C PHE* 1.3 76.0 - - - +
312C ASP* 1.3 71.4 + - - +
314C LEU* 3.5 5.7 + - - +
315C GLY* 3.2 17.3 + - - -
326C TYR* 4.5 6.5 + - + -
338C PHE* 3.6 33.6 - - + -
32D VAL* 3.8 32.3 - - - +
78D VAL* 6.2 3.8 - - - -
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Residues in contact with ASP 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C GLU* 3.1 23.1 + - - +
309C ALA* 3.8 7.2 - - - +
311C ARG* 1.3 86.2 + - - +
313C ALA* 1.3 59.8 + - - +
315C GLY* 3.4 2.6 + - - +
316C LYS* 3.0 43.5 + - - +
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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 ALA 2.9 17.4 + - - +
310C PHE 3.6 5.8 - - - +
312C ASP* 1.3 74.4 - - - +
314C LEU* 1.3 62.4 + - - +
316C LYS* 3.3 3.9 + - - +
317C LEU* 3.0 35.3 + - - +
355C LEU* 4.3 5.4 - - + -
359C TYR* 3.6 46.2 - - + -
361C LEU* 4.3 7.0 - - + -
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Residues in contact with LEU 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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299C LEU* 5.9 0.4 - - + -
310C PHE* 3.0 36.5 + - + +
311C ARG 3.8 4.3 - - - +
313C ALA* 1.3 76.6 - - - +
315C GLY* 1.3 54.8 + - - +
317C LEU* 3.4 13.3 + - + +
318C SER* 2.9 30.3 + - - -
324C LEU* 4.4 18.1 - - + +
326C TYR* 3.8 42.2 - - + -
338C PHE* 3.5 44.2 - - + -
340C CYS* 4.5 7.4 - - - -
351C ILE* 5.3 3.1 - - + -
355C LEU* 5.0 6.5 - - + -
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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
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311C ARG 3.2 11.4 + - - -
312C ASP* 3.7 4.7 - - - -
313C ALA 3.3 0.2 - - - -
314C LEU* 1.3 78.1 - - - +
316C LYS* 1.3 60.5 + - - +
318C SER* 3.2 14.1 + - - -
319C LEU* 3.4 18.3 + - - +
326C TYR* 3.6 13.9 + - - -
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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
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312C ASP* 3.0 28.9 + - - +
313C ALA* 3.3 5.4 + - - +
315C GLY* 1.3 71.5 - - - +
317C LEU* 1.3 67.4 + - - +
318C SER 3.4 0.3 + - - -
319C LEU* 3.4 27.3 + - + +
320C ASN* 4.2 5.7 + - - +
359C TYR* 3.5 41.3 - - + +
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Residues in contact with LEU 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C ALA 3.0 13.7 + - - +
314C LEU* 3.6 9.2 - - + +
316C LYS* 1.3 75.8 - - - +
318C SER* 1.3 57.5 + - - +
320C ASN* 3.2 6.4 + - - +
321C ASP* 2.9 31.3 + - + +
324C LEU* 3.8 17.5 - - + -
351C ILE* 4.1 25.4 - - + +
354C ARG* 3.0 38.1 + - + +
355C LEU* 3.6 29.2 - - + -
359C TYR* 3.4 31.0 - - + +
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Residues in contact with SER 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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266C HIS* 3.4 14.0 - - - -
314C LEU 2.9 17.6 + - - -
315C GLY* 3.4 10.1 - - - -
316C LYS 3.2 0.6 - - - -
317C LEU* 1.3 75.1 - - - +
319C LEU* 1.3 62.5 + - - +
320C ASN 3.1 1.0 + - - -
321C ASP* 3.5 23.1 + - - +
324C LEU* 4.6 10.9 + - - +
326C TYR* 3.4 24.9 - - - -
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Residues in contact with LEU 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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264C ASP* 5.2 9.2 - - + +
265C ILE* 2.5 41.9 - - + +
266C HIS* 2.9 47.3 + - + +
315C GLY 3.6 13.7 - - - +
316C LYS* 3.7 20.0 - - + +
317C LEU 3.2 0.6 - - - -
318C SER* 1.3 77.5 - - - +
320C ASN* 1.3 55.8 + - - +
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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
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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