Contacts of the helix formed by residues 318 - 332 (chain E) in PDB entry 4O9U
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 LEU 318 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E VAL* 3.6 20.0 - - + -
141E TYR* 3.7 32.5 - - + -
142E LEU* 3.7 16.6 - - + -
314E LEU 3.3 3.4 + - - -
315E PRO 3.2 3.1 - - - -
317E GLU* 1.3 75.6 - - - +
319E SER* 1.3 62.3 + - - +
320E VAL 3.3 4.4 + - - -
321E HIS* 3.7 2.5 + - + -
322E ALA* 3.3 21.5 + - - +
148F ALA 4.7 0.4 - - - +
151F SER 3.1 28.0 - - - +
152F PRO 3.4 16.8 - - - +
153F ARG 3.6 13.0 - - - +
154F PHE* 3.6 38.6 - - + -
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Residues in contact with SER 319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E ARG* 3.1 35.4 + - - -
16E ARG* 4.9 0.7 - - - -
43E GLY 2.7 19.1 + - - -
44E ALA* 3.4 5.4 - - - +
45E TYR* 4.3 6.2 - - - -
315E PRO 3.1 10.5 - - - -
316E SER 3.2 17.0 + - - -
317E GLU 3.3 2.2 + - - -
318E LEU* 1.3 75.3 - - - +
320E VAL* 1.3 65.0 + - - +
322E ALA* 4.1 0.9 - - - -
323E SER* 2.7 31.4 + - - -
152F PRO* 4.1 2.2 + - - +
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Residues in contact with VAL 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E ALA* 3.7 25.1 - - - +
45E TYR* 3.9 18.4 - - + -
46E HIS* 4.7 15.2 + - + +
318E LEU 3.3 1.6 + - - -
319E SER* 1.3 78.8 - - - +
321E HIS* 1.3 68.6 + - + +
323E SER* 4.1 2.4 - - - -
324E GLU* 3.4 22.7 + - - +
152F PRO* 3.7 32.5 - - + +
153F ARG* 4.4 26.7 - - + +
277F PRO 5.4 1.8 - - - +
278F GLY* 5.4 2.7 - - - -
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Residues in contact with HIS 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318E LEU* 3.7 5.3 + - + +
320E VAL* 1.3 81.6 - - + +
322E ALA* 1.3 60.6 + - - +
324E GLU* 3.2 21.3 + - - +
325E MET* 2.8 34.8 + - - +
152F PRO 4.1 2.3 + - - +
153F ARG* 3.7 39.8 + - + -
154F PHE* 3.1 56.2 + + + -
165F ILE* 3.8 37.3 - - + +
166F ARG* 4.5 9.3 + - - +
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Residues in contact with ALA 322 (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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16E ARG* 4.6 3.6 - - - -
135E GLN* 3.3 28.0 + - - +
138E VAL* 3.9 22.5 - - + +
315E PRO* 3.5 21.8 - - + +
318E LEU 3.3 18.9 + - - +
319E SER* 4.3 1.3 - - - +
321E HIS* 1.3 78.5 - - - +
323E SER* 1.3 58.1 + - - +
325E MET* 3.4 3.0 + - - +
326E TYR* 2.9 23.8 + - - +
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Residues in contact with SER 323 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E ARG* 3.8 10.8 - - - +
17E VAL* 3.5 33.7 + - - +
20E VAL* 4.0 12.3 - - - +
44E ALA* 3.5 18.6 - - - +
319E SER 2.7 22.9 + - - -
320E VAL 4.1 1.1 - - - -
322E ALA* 1.3 74.5 - - - +
324E GLU* 1.3 60.1 + - - +
326E TYR* 3.0 6.7 + - - +
327E ALA* 2.8 32.1 + - - +
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Residues in contact with GLU 324 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E VAL* 4.0 24.2 - - + +
22E GLU* 5.7 5.8 - - + +
23E VAL* 6.1 0.4 - - + -
46E HIS* 5.1 9.1 + - - +
320E VAL* 3.4 16.3 + - - +
321E HIS* 3.2 29.5 + - - +
323E SER* 1.3 79.9 - - - +
325E MET* 1.3 60.5 + - + +
326E TYR 3.5 0.2 + - - -
327E ALA* 3.6 7.6 + - - +
328E LYS* 3.6 27.7 + - + +
162F ALA 5.3 0.8 - - - +
164F THR 5.3 3.3 - - - +
165F ILE* 4.6 9.3 - - + +
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Residues in contact with MET 325 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B PRO* 5.7 0.4 - - + -
134E SER* 3.7 40.2 - - - +
135E GLN* 4.2 2.2 - - - +
137E THR* 4.6 9.2 - - + +
138E VAL* 4.3 13.7 - - - -
321E HIS 2.8 20.5 + - - +
322E ALA 3.7 4.9 - - - +
324E GLU* 1.3 76.8 - - + +
326E TYR* 1.3 59.4 + - - +
328E LYS 4.1 0.2 + - - -
329E ASN* 2.9 29.6 + - - +
154F PHE* 4.6 9.9 - - - -
158F LEU* 6.5 0.2 - - - -
160F THR* 3.7 32.3 - - + +
162F ALA* 3.6 29.4 - - + +
165F ILE* 4.2 21.5 - - + -
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Residues in contact with TYR 326 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E ARG* 5.7 3.6 - - - -
17E VAL 4.3 2.5 - - - -
18E ALA* 3.4 43.1 - - + -
73E THR 2.5 24.3 + - - -
74E VAL* 3.5 23.5 + - + -
93E GLY* 3.8 11.3 - - - -
94E PHE* 4.0 22.1 + + - -
117E MET* 4.7 7.0 - - + +
131E ALA* 4.7 14.1 - - + -
135E GLN* 3.7 23.1 - - + +
322E ALA 2.9 17.4 + - - +
323E SER* 3.0 7.6 + - - +
325E MET* 1.3 78.9 - - - +
327E ALA* 1.3 62.8 + - - +
329E ASN* 3.4 7.2 - - + +
330E LEU* 3.3 37.8 + - + +
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Residues in contact with ALA 327 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E ALA 3.4 18.2 - - - +
19E LEU* 3.9 5.1 - - + +
20E VAL* 3.7 26.5 - - + +
23E VAL* 3.6 23.9 - - + +
323E SER 2.8 14.6 + - - +
324E GLU 3.6 1.8 + - - +
325E MET 3.4 0.2 - - - -
326E TYR* 1.3 75.6 - - - +
328E LYS* 1.3 60.5 + - - +
330E LEU* 3.3 6.7 + - - +
331E TYR* 2.9 23.7 + - - +
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Residues in contact with LYS 328 (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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359B GLU* 5.7 1.2 + - - -
22E GLU* 3.7 15.8 + - - -
23E VAL* 3.6 14.3 - - + +
26E ARG* 3.1 37.8 - - - +
128E SER 4.3 2.0 - - - -
324E GLU* 3.6 20.7 + - + +
325E MET 4.6 3.1 - - - +
326E TYR 3.4 0.2 - - - -
327E ALA* 1.3 73.9 - - - +
329E ASN* 1.3 58.6 + - - +
330E LEU 3.1 0.7 - - - -
331E TYR* 3.5 12.5 - - + +
332E ASN* 2.7 44.5 + - - +
162F ALA* 4.6 11.9 - - + +
163F GLY* 4.5 24.2 - - - +
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Residues in contact with ASN 329 (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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117E MET* 4.3 11.6 - - + +
127E GLN 4.7 1.4 + - - -
128E SER 3.2 21.5 + - - -
129E MET* 3.4 33.2 - - - +
130E ASP 3.8 5.1 + - - +
131E ALA* 3.6 7.9 - - + +
134E SER* 2.9 28.1 + - - -
325E MET 2.9 14.9 + - - +
326E TYR* 3.4 13.6 + - + +
328E LYS* 1.3 77.3 - - - +
330E LEU* 1.3 58.6 + - - +
333E LEU* 3.1 25.5 + - - +
161F ALA 5.5 0.2 - - - -
162F ALA* 4.3 11.3 - - - +
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Residues in contact with LEU 330 (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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18E ALA* 3.2 28.3 - - + +
19E LEU* 3.8 4.9 - - + -
72E PHE* 3.6 47.3 - - + -
92E VAL* 3.8 29.6 - - + -
117E MET* 4.8 10.8 - - + -
326E TYR* 3.3 34.9 + - + +
327E ALA 3.3 6.9 + - - +
328E LYS 3.1 0.2 - - - -
329E ASN* 1.3 79.2 - - + +
331E TYR* 1.3 53.7 + - - +
333E LEU* 3.2 6.0 + - + +
334E SER* 2.6 34.6 + - - -
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Residues in contact with TYR 331 (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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23E VAL* 3.7 17.5 - - + -
26E ARG* 3.6 57.1 + - + +
27E LEU* 3.6 42.0 - - + -
30E GLY* 5.8 1.2 - - - -
327E ALA 2.9 14.2 + - - +
328E LYS* 3.0 15.2 + - + +
330E LEU* 1.3 72.9 - - - +
332E ASN* 1.3 72.7 + - - +
333E LEU 3.1 1.3 - - - -
334E SER* 2.5 30.9 + - - -
335E SER* 3.4 4.3 + - - -
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Residues in contact with ASN 332 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B GLY 5.5 0.9 - - - +
395B PRO* 5.3 7.2 - - - +
128E SER* 3.3 52.3 + - - +
129E MET* 3.2 20.3 - - + +
328E LYS* 2.7 23.8 + - - +
331E TYR* 1.3 84.1 - - - +
333E LEU* 1.3 57.1 + - - +
335E SER* 3.2 23.3 - - - -
336E LEU* 4.3 0.3 - - - +
161F ALA 4.6 5.5 + - - -
162F ALA* 6.1 0.2 - - - +
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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