Contacts of the helix formed by residues 299 - 316 (chain E) in PDB entry 3EGC
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 PRO 299 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E SER* 3.9 12.6 - - - +
297E GLU* 4.3 2.2 - - - +
298E GLN* 1.4 84.0 - - + +
300E THR* 1.3 59.6 + - - +
301E ARG 3.3 2.5 - - - -
302E ARG* 3.2 17.9 + - + -
303E ILE* 2.8 30.9 + - + +
326E LEU* 3.8 22.7 - - + -
327E GLN 3.1 30.5 - - - +
328E THR* 4.4 1.1 - - + -
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Residues in contact with THR 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E PHE* 3.6 42.6 - - + +
84E GLU* 2.7 43.3 + - - +
85E VAL* 3.5 12.4 - - - +
281E ASP* 5.7 0.4 - - - +
298E GLN* 3.1 16.1 + - + +
299E PRO* 1.3 74.7 - - - +
301E ARG* 1.3 74.6 + - - +
303E ILE* 3.3 11.4 + - - +
304E GLY 3.1 16.5 + - - -
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Residues in contact with ARG 301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E GLU* 3.5 50.7 + - - +
87E SER* 4.6 1.1 - - - +
88E GLY* 3.4 17.7 - - - +
299E PRO 3.3 0.2 - - - -
300E THR* 1.3 83.9 + - - +
302E ARG* 1.3 58.9 + - - +
304E GLY 3.1 1.9 + - - -
305E GLN* 2.8 27.2 + - - +
78F GLU* 2.9 43.7 + - - +
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Residues in contact with ARG 302 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299E PRO* 3.2 19.3 + - + +
301E ARG* 1.3 77.7 - - - +
303E ILE* 1.3 66.4 + - - +
305E GLN* 3.6 22.7 + - - -
306E GLU* 2.6 62.0 + - + +
309E ARG* 4.1 7.6 - - - +
324E MET* 5.2 4.1 - - - +
326E LEU* 3.9 17.9 - - + -
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Residues in contact with ILE 303 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E PHE* 4.4 19.3 - - + -
85E VAL* 4.4 9.0 - - + -
152E VAL* 3.7 27.4 - - + -
153E ASN* 4.7 3.4 - - - +
164E VAL* 3.8 20.4 - - + +
165E LEU* 5.2 0.9 - - - -
166E SER* 3.5 27.6 - - - +
299E PRO* 2.8 33.3 + - + +
300E THR* 3.4 13.2 - - - +
302E ARG* 1.3 73.3 - - - +
304E GLY* 1.4 55.6 + - - +
307E ALA* 3.0 29.8 + - - +
326E LEU* 3.7 21.9 - - + +
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Residues in contact with GLY 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E VAL* 3.2 31.1 - - - +
89E VAL* 3.2 27.1 - - - +
300E THR 3.1 7.3 + - - -
301E ARG 3.1 6.9 + - - -
303E ILE* 1.4 76.9 - - - +
305E GLN* 1.3 61.5 + - - +
307E ALA* 3.4 1.8 + - - +
308E MET 3.1 18.9 + - - -
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Residues in contact with GLN 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E GLY* 3.7 16.4 - - - +
91E SER* 5.9 2.8 + - - -
92E GLU* 3.4 25.4 + - + +
301E ARG 2.8 15.8 + - - +
302E ARG* 3.3 25.7 + - - +
304E GLY* 1.3 75.0 - - - +
306E GLU* 1.3 58.2 + - - +
308E MET* 3.4 4.3 + - - +
309E ARG* 2.9 65.0 + - - +
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Residues in contact with GLU 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E VAL* 4.1 8.8 - - + +
302E ARG* 2.6 67.4 + - + +
303E ILE 4.2 2.0 - - - +
305E GLN* 1.3 69.6 - - - +
307E ALA* 1.3 61.1 + - - +
309E ARG* 3.1 30.0 + - - +
310E MET* 2.8 28.8 + - - +
324E MET* 3.4 42.3 - - + +
326E LEU* 4.5 2.2 - - + -
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Residues in contact with ALA 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128E ILE* 4.0 13.0 - - + -
150E VAL* 3.5 23.5 - - + +
152E VAL* 3.6 20.4 - - + -
164E VAL* 3.5 12.0 - - + +
303E ILE 3.0 20.1 + - - +
304E GLY* 3.7 4.5 - - - +
306E GLU* 1.3 74.6 - - - +
308E MET* 1.3 54.6 + - - +
310E MET* 3.1 3.5 + - - +
311E LEU* 2.7 35.9 + - - +
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Residues in contact with MET 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E VAL* 3.5 35.9 - - + -
89E VAL* 2.9 39.9 - - + +
92E GLU* 3.8 11.7 - - + -
93E ALA* 3.6 39.0 - - + +
98E TYR* 5.5 0.7 - - - -
100E VAL* 4.3 2.5 - - + -
128E ILE* 3.4 15.8 - - + +
304E GLY 3.1 14.7 + - - +
305E GLN 3.6 4.3 - - - +
307E ALA* 1.3 79.8 - - - +
309E ARG* 1.3 56.7 + - - +
311E LEU* 3.8 5.0 - - - +
312E ILE* 2.9 45.5 + - + +
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Residues in contact with ARG 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E GLU* 3.3 31.4 + - - +
96E LYS* 3.9 9.4 - - - +
302E ARG* 4.1 7.1 - - - +
305E GLN* 2.9 46.3 + - - +
306E GLU* 3.1 37.6 + - - +
307E ALA 3.3 0.4 - - - -
308E MET* 1.3 71.7 - - - +
310E MET* 1.3 67.8 + - - +
312E ILE* 3.4 5.9 + - - +
313E HIS* 3.0 38.4 + - + +
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Residues in contact with MET 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150E VAL* 3.4 15.5 - - + -
162E GLY* 2.1 54.3 - - - +
163E ALA 3.2 6.5 - - - +
164E VAL* 4.9 4.0 - - + -
306E GLU 2.8 19.8 + - - +
307E ALA* 3.6 3.6 - - - +
309E ARG* 1.3 79.1 - - - +
311E LEU* 1.3 61.2 + - - +
313E HIS* 3.5 8.7 + - - +
314E MET* 3.2 28.8 + - - +
320E ASN 4.1 10.5 - - - +
321E ALA* 3.8 4.5 - - + -
322E THR* 3.2 32.8 - - + +
324E MET* 5.8 6.3 - - - +
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Residues in contact with LEU 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E VAL* 3.5 42.8 - - + -
126E GLY* 3.7 10.3 - - - -
127E LEU 3.6 10.8 - - - +
128E ILE* 3.7 15.7 - - + -
148E PRO* 3.3 39.7 - - + +
150E VAL* 3.7 18.7 - - + +
307E ALA 2.7 20.2 + - - +
308E MET* 3.8 8.5 - - - +
310E MET* 1.3 72.8 - - - +
312E ILE* 1.3 62.7 + - - +
314E MET* 3.2 4.0 + - - +
315E ILE* 3.1 33.4 + - + +
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Residues in contact with ILE 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E GLU* 4.4 2.2 - - + +
93E ALA* 4.9 0.4 - - - -
96E LYS* 3.6 55.0 - - + +
98E TYR* 3.9 21.3 - - + +
308E MET* 2.9 42.0 + - + +
309E ARG* 3.9 5.4 - - - +
310E MET 3.3 0.2 - - - -
311E LEU* 1.3 74.2 - - - +
313E HIS* 1.3 63.3 - - + +
315E ILE* 3.2 8.7 + - + +
316E GLU* 2.9 55.2 + - - +
318E THR* 5.8 0.4 - - - +
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Residues in contact with HIS 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E LYS* 6.0 3.4 - - - -
309E ARG* 3.0 34.7 + - + +
310E MET* 3.8 7.4 - - - +
312E ILE* 1.3 79.7 - - + +
314E MET* 1.3 58.0 + - - +
317E GLY* 2.8 25.6 + - - -
318E THR* 2.8 42.8 + - - -
319E GLY* 3.5 25.2 + - - -
320E ASN 4.9 1.6 - - - +
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Residues in contact with MET 314 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E PRO* 3.7 34.4 - - + +
149E ILE 3.9 10.1 - - - +
150E VAL* 3.7 20.4 - - - -
160E GLY 3.9 10.5 - - - +
310E MET* 3.2 25.9 + - - +
311E LEU* 3.5 7.2 - - - +
312E ILE 3.2 0.8 - - - -
313E HIS* 1.3 78.1 - - - +
315E ILE* 1.3 61.5 + - - +
317E GLY* 3.6 7.3 + - - -
319E GLY 4.0 6.5 - - - +
320E ASN* 4.1 4.9 - - - -
321E ALA* 3.7 39.3 - - + +
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Residues in contact with ILE 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E ARG 4.6 9.0 - - - +
70E VAL* 3.9 21.5 - - + -
98E TYR* 3.9 22.7 - - + +
125E ASP* 3.5 52.3 - - + +
148E PRO* 3.7 11.2 - - + -
311E LEU* 3.1 23.8 + - + +
312E ILE* 3.2 7.4 + - + +
314E MET* 1.3 80.3 - - - +
316E GLU* 1.3 62.9 + - + +
317E GLY 3.2 1.6 + - - -
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Residues in contact with GLU 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E ASN* 5.3 0.7 + - - -
96E LYS* 5.5 1.2 - - - +
98E TYR* 2.6 38.0 + - - +
312E ILE* 2.9 28.1 + - - +
315E ILE* 1.3 77.6 - - + +
317E GLY* 1.3 63.6 + - - +
318E THR* 3.4 21.9 + - + +
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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
------------------------------------------------------------
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