Contacts of the helix formed by residues 302 - 319 (chain A) in PDB entry 3D8U
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 302 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A PHE* 1.3 71.4 - - - +
303A TYR* 1.3 60.9 + - - +
304A GLU* 3.0 32.0 - - - +
305A ARG* 3.2 28.3 + - + +
306A MSE 2.8 26.2 + - - +
329A MSE 4.0 10.2 - - + +
330A GLY 5.4 1.8 + - - -
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Residues in contact with TYR 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LYS* 4.1 8.5 - - + -
84A ALA* 3.7 39.3 - - + +
87A HIS* 3.3 31.2 - + + +
88A PHE* 3.1 18.6 - - - +
155A ILE* 6.3 0.7 - - + -
169A VAL* 5.3 6.6 - - + +
171A HIS* 5.5 4.2 - - - -
284A GLU* 4.0 19.0 + - + +
285A GLY 6.2 0.2 - - - -
301A PHE* 3.5 45.4 + + + -
302A ASP* 1.3 71.3 - - - +
304A GLU* 1.3 60.3 + - - +
306A MSE 3.4 24.8 - - + +
307A GLY 2.8 23.0 + - - -
329A MSE 3.7 17.9 - - + -
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Residues in contact with GLU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A HIS* 3.7 31.5 - - - +
91A SER* 2.6 36.1 + - - -
301A PHE 3.9 4.0 - - - +
302A ASP* 3.0 23.7 - - - +
303A TYR* 1.3 105.2 + - - +
305A ARG* 1.3 58.1 + - - +
307A GLY 2.9 0.2 + - - -
308A THR* 2.8 17.2 + - - -
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Residues in contact with ARG 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A ASP* 3.2 38.8 + - + +
304A GLU* 1.3 76.7 - - - +
306A MSE 1.3 52.7 + - - +
308A THR* 3.4 10.2 + - - -
309A LYS* 2.7 47.7 + - + +
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Residues in contact with MSE 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ALA* 4.6 4.3 - - + +
88A PHE* 3.3 37.5 - - + -
133A PHE* 5.2 2.0 - - + -
155A ILE* 3.9 32.5 - - + -
167A ILE* 5.0 15.5 - - + +
168A GLY* 6.2 0.4 - - - -
169A VAL* 5.5 3.1 - - - -
302A ASP 2.8 18.4 + - - +
303A TYR* 3.4 32.5 - - + +
305A ARG* 1.3 72.5 - - - +
307A GLY* 1.3 67.6 + - - +
309A LYS* 2.9 6.3 + - - +
310A ALA* 2.9 28.2 + - + +
329A MSE 3.5 30.7 - - - +
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Residues in contact with GLY 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PHE* 3.3 33.4 - - - -
91A SER* 3.5 5.2 - - - -
92A PHE* 3.1 31.5 - - - -
303A TYR 2.8 18.3 + - - -
304A GLU 2.9 5.2 + - - -
306A MSE 1.3 73.3 - - - +
308A THR* 1.3 61.1 + - - +
310A ALA* 3.6 0.9 - - - +
311A ALA* 3.7 0.5 + - - +
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Residues in contact with THR 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A SER* 3.0 19.0 + - - -
95A ALA* 4.1 18.7 - - + +
304A GLU 2.8 14.4 + - - -
305A ARG* 3.6 12.3 - - - +
306A MSE 3.0 0.2 + - - -
307A GLY* 1.3 67.4 - - - +
309A LYS* 1.3 56.7 + - + +
310A ALA 2.6 16.9 + - - -
311A ALA* 2.8 18.2 + - - +
312A GLU* 3.4 33.1 + - + +
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Residues in contact with LYS 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A ARG* 2.7 32.6 + - + +
306A MSE 2.9 5.1 + - - +
308A THR* 1.3 73.7 - - - +
310A ALA* 1.3 61.1 + - - +
312A GLU* 4.2 12.2 - - - +
313A LYS* 3.6 23.0 + - - +
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Residues in contact with ALA 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A PHE* 4.0 11.0 - - + -
92A PHE* 3.7 17.0 - - + -
131A VAL* 5.5 0.2 - - + -
153A LEU* 4.0 26.5 - - + +
167A ILE* 5.7 5.4 - - + -
306A MSE 2.9 17.5 + - + +
307A GLY 3.6 6.7 - - - +
308A THR 2.6 5.3 + - - -
309A LYS* 1.3 72.2 - - - +
311A ALA* 1.3 66.7 + - - +
313A LYS* 3.0 15.0 + - - +
314A LEU* 3.0 11.8 + - - +
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Residues in contact with ALA 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PHE* 3.8 31.2 - - + +
95A ALA* 4.7 6.7 - - + -
96A LEU* 4.3 14.8 - - + +
307A GLY 3.7 2.3 + - - +
308A THR 2.8 14.0 + - - +
310A ALA* 1.3 72.7 - - - +
312A GLU* 1.3 53.8 + - + +
314A LEU* 2.8 9.0 + - - +
315A LEU* 2.7 51.8 + - + +
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Residues in contact with GLU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ALA* 6.2 1.6 - - + -
308A THR* 3.4 32.1 - - + +
309A LYS* 4.2 11.7 - - - +
310A ALA 3.3 0.2 - - - -
311A ALA* 1.3 75.1 - - + +
313A LYS* 1.3 53.0 + - - +
315A LEU* 3.6 6.6 - - - +
316A HIS* 2.7 39.2 + - - +
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Residues in contact with LYS 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LEU* 4.0 22.0 - - + -
165A LEU* 4.3 29.1 - - + +
166A ASN 3.5 23.3 + - - +
167A ILE* 5.3 5.6 - - + -
309A LYS 3.6 13.3 + - - +
310A ALA 3.0 11.5 + - - +
312A GLU* 1.3 80.6 - - - +
314A LEU* 1.3 57.6 + - - +
316A HIS* 3.3 9.0 + - - +
317A ALA* 2.9 29.2 + - - +
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Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ILE* 4.9 11.9 - - + -
92A PHE* 4.6 10.5 - - + -
96A LEU* 5.7 1.6 - - + -
129A GLY* 4.8 5.6 - - - -
130A VAL 4.3 13.0 - - - +
131A VAL* 3.5 30.5 - - + -
151A PRO* 3.9 23.6 - - + +
152A VAL 4.2 2.5 - - - -
153A LEU* 3.8 31.4 - - + +
165A LEU* 5.1 6.3 - - + -
310A ALA 3.0 7.0 + - - +
311A ALA* 2.8 13.8 + - - +
313A LYS* 1.3 76.1 - - - +
315A LEU* 1.3 52.8 + - + +
317A ALA* 3.0 6.1 + - - +
318A ILE* 2.7 44.0 + - + +
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Residues in contact with LEU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ALA 5.7 0.7 - - - +
96A LEU* 3.7 29.2 - - + -
99A ALA* 3.6 38.4 - - + +
101A TYR* 6.2 0.9 - - + -
311A ALA* 2.7 42.3 + - + +
312A GLU* 3.7 7.0 - - - +
314A LEU* 1.3 73.2 - - + +
316A HIS* 1.3 64.9 + - - +
317A ALA 3.2 0.3 + - - -
318A ILE* 3.3 33.5 + - + +
319A LYS 3.9 5.5 - - - +
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Residues in contact with HIS 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A GLU 2.7 23.8 + - - +
313A LYS* 3.5 8.1 - - - +
315A LEU* 1.3 71.8 - - - +
317A ALA* 1.3 63.0 + - + +
319A LYS 3.2 14.8 - - - +
320A GLY* 3.6 11.1 - - - -
321A GLU* 2.9 50.5 + - + +
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Residues in contact with ALA 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A PRO* 4.5 11.4 - - + -
165A LEU* 3.8 28.3 - - + -
313A LYS 2.9 13.5 + - - +
314A LEU* 3.0 10.0 + - - +
316A HIS* 1.3 78.9 - - + +
318A ILE* 1.3 68.3 + - - +
319A LYS* 2.7 10.5 + - - -
320A GLY 3.8 7.9 + - - +
321A GLU 5.4 2.5 - - - -
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Residues in contact with ILE 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ALA* 4.2 15.5 - - + +
129A GLY* 5.0 2.5 - - - -
151A PRO* 4.1 26.3 - - + +
314A LEU* 2.7 37.6 + - + +
315A LEU* 3.3 25.8 - - + +
317A ALA* 1.3 70.7 - - - +
319A LYS* 1.3 67.6 + - + +
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Residues in contact with LYS 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A LEU 3.9 5.4 - - - +
316A HIS* 3.2 10.7 - - - +
317A ALA 2.7 3.2 + - - -
318A ILE* 1.3 86.7 - - + +
320A GLY* 1.3 58.4 + - - +
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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
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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