Contacts of the helix formed by residues 313 - 329 (chain B) in PDB entry 4EVI
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 313 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A HIS* 3.4 23.4 + - - -
311B ASN 3.8 1.0 + - - -
312B ASP* 1.3 74.5 - - - +
314B ASN* 1.3 64.8 + - - +
316B MET* 4.3 3.6 - - - -
317B GLY* 2.8 26.3 + - - -
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Residues in contact with ASN 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A HIS* 4.9 3.7 + - - -
312B ASP* 3.3 9.5 + - - +
313B SER* 1.3 88.0 + - - +
315B SER* 1.3 62.5 + - - +
317B GLY* 3.3 1.5 + - - -
318B THR* 3.2 25.5 + - - -
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Residues in contact with SER 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PRO* 6.3 0.4 - - - -
310B CYS* 3.4 19.3 - - - -
312B ASP* 2.8 34.1 + - - -
314B ASN* 1.3 76.3 - - - +
316B MET* 1.3 58.0 + - - +
318B THR* 3.3 3.1 + - - -
319B SER* 2.9 32.9 + - - -
360B LEU* 3.5 23.2 - - - +
403B GOL 3.7 17.8 - - - -
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Residues in contact with MET 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A HIS* 3.9 13.5 - - + +
305B LEU* 3.5 41.7 - - + +
306B ASP* 4.6 7.9 - - + -
310B CYS 4.0 8.4 + - - +
311B ASN* 4.7 11.9 - - + +
312B ASP 2.8 16.7 + - - +
313B SER* 3.8 6.7 - - - +
315B SER* 1.3 75.1 - - - +
317B GLY* 1.3 57.8 + - - +
319B SER* 3.3 2.6 + - - -
320B LEU* 2.9 61.1 + - + +
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Residues in contact with GLY 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A HIS* 4.4 11.9 - - - -
73A MET* 5.0 0.5 - - - +
76A HIS* 3.3 27.7 + - - -
313B SER 2.8 13.8 + - - -
314B ASN* 3.8 2.0 - - - -
316B MET* 1.3 78.3 - - - +
318B THR* 1.3 56.1 + - - +
320B LEU* 3.3 3.3 + - - +
321B ILE* 2.9 32.4 + - - +
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Residues in contact with THR 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A PRO* 3.7 26.6 + - + +
17A TRP* 4.4 15.0 - - + -
18A HIS* 2.9 32.7 + - + +
21A LEU* 6.0 0.2 - - + -
314B ASN 3.2 13.3 + - - -
315B SER* 3.8 7.4 - - - -
317B GLY* 1.3 74.6 - - - +
319B SER* 1.3 59.4 + - - +
321B ILE* 3.2 6.7 + - + +
322B LEU* 2.9 30.6 + - + +
360B LEU* 3.7 20.2 - - + -
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Residues in contact with SER 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B HIS* 4.7 1.0 + - - -
305B LEU* 3.5 28.6 + - - +
310B CYS* 4.9 5.9 + - - -
315B SER 2.9 20.7 + - - -
316B MET* 3.3 8.2 + - - -
318B THR* 1.3 76.0 - - - +
320B LEU* 1.3 58.0 + - - +
322B LEU* 3.2 2.2 + - - -
323B ASP* 2.9 24.1 + - - +
334B LEU* 3.3 24.1 - - - +
360B LEU* 3.8 23.7 + - - +
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Residues in contact with LEU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ARG 6.0 0.2 - - - +
72A ARG* 3.7 48.2 - - + +
73A MET* 3.9 16.3 - - + +
76A HIS* 3.5 35.2 - - + -
305B LEU* 4.2 19.1 - - + -
316B MET* 2.9 37.3 + - + +
317B GLY* 3.8 4.0 - - - +
319B SER* 1.3 73.2 - - - +
321B ILE* 1.3 60.5 + - - +
323B ASP* 3.2 8.8 + - + +
324B MET* 3.0 31.7 + - - +
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Residues in contact with ILE 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A HIS* 3.5 42.6 - - + +
21A LEU* 3.5 43.1 - - + +
24A ILE* 4.1 14.6 - - + +
25A ASN* 3.7 18.4 - - - +
73A MET* 3.5 24.0 - - + -
317B GLY 2.9 13.8 + - - +
318B THR* 3.2 10.5 + - + +
320B LEU* 1.3 74.0 - - - +
322B LEU* 1.3 59.2 + - - +
324B MET* 3.2 4.2 + - - +
325B LEU* 2.9 25.8 + - - +
404B GOL 5.2 0.2 - - - -
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Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A TRP* 3.9 26.9 - - + -
21A LEU* 3.7 24.7 - - + -
268B TRP* 5.3 1.8 - - + -
303B HIS* 3.6 31.4 - - + +
318B THR* 2.9 20.8 + - + +
319B SER 3.5 6.5 - - - +
321B ILE* 1.3 76.2 - - - +
323B ASP* 1.3 53.2 + - - +
325B LEU* 3.2 6.2 + - + +
326B PHE* 2.7 44.4 + - + -
334B LEU* 4.0 13.0 - - + -
360B LEU* 4.0 7.2 - - + -
401B N7I 3.8 27.6 - - + -
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Residues in contact with ASP 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ARG* 2.9 52.1 + - - +
72A ARG* 3.0 24.5 + - - +
305B LEU* 6.0 0.4 - - + -
319B SER 2.9 13.3 + - - +
320B LEU* 3.2 16.3 + - + +
322B LEU* 1.3 77.1 - - - +
324B MET* 1.3 62.0 + - + +
326B PHE* 3.8 1.3 - - - -
327B MET* 2.8 23.0 + - - +
333B SER* 3.2 3.8 - - - -
334B LEU* 2.9 36.0 + - + +
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Residues in contact with MET 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ILE* 3.6 15.7 - - + -
28A THR* 3.9 17.7 - - + -
69A ARG* 3.3 43.5 - - + +
70A LEU* 3.7 16.2 - - - +
73A MET* 3.9 22.9 - - + -
131B TRP* 3.3 17.5 - - + -
320B LEU 3.0 17.4 + - - +
321B ILE 3.5 7.6 - - - +
323B ASP* 1.3 81.3 - - + +
325B LEU* 1.3 65.9 + - - +
327B MET* 3.2 26.6 + - + +
328B SER 3.0 18.0 + - - -
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Residues in contact with LEU 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 4.2 17.5 - - + -
23A TYR* 3.9 22.0 - - - +
24A ILE* 4.3 12.2 - - + +
122B SER* 5.8 0.2 - - - -
127B LEU* 4.7 11.4 - - + +
131B TRP* 5.4 0.7 - - - +
321B ILE 2.9 14.2 + - - +
322B LEU* 3.4 8.7 - - + +
324B MET* 1.3 74.8 - - - +
326B PHE* 1.3 69.4 + - + +
328B SER* 2.8 27.6 + - - +
329B PHE* 3.2 32.5 + - + -
401B N7I 3.5 46.7 - - + +
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Residues in contact with PHE 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B TRP* 4.7 5.8 - - - -
271B CYS* 3.8 38.8 - - + -
303B HIS* 5.0 4.0 - + - -
322B LEU* 2.7 30.6 + - + +
323B ASP* 3.8 4.9 - - - +
325B LEU* 1.3 81.8 - - + +
327B MET* 1.3 62.9 + - - +
330B LEU* 2.9 51.2 + - + +
332B GLY 4.0 15.1 - - - +
333B SER 4.5 2.2 - - - +
334B LEU* 3.5 28.7 - - + -
401B N7I 3.6 50.3 - + + -
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Residues in contact with MET 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A PHE* 3.6 59.9 - - + +
69A ARG* 3.4 18.5 - - - +
70A LEU* 4.8 7.9 - - + -
131B TRP* 4.6 3.8 - - + -
134B MET* 4.1 30.2 - - + +
137B TRP* 5.0 7.6 - - + -
138B LEU* 5.3 3.4 - - + -
150B ASN* 3.8 14.2 - - - +
151B ALA 4.8 0.7 + - - -
323B ASP 2.8 22.0 + - - +
324B MET* 3.2 34.5 + - + +
326B PHE* 1.3 74.1 - - - +
328B SER* 1.3 62.3 + - - +
330B LEU 4.1 2.0 - - - +
331B GLU* 6.4 0.2 - - - +
332B GLY 4.4 2.0 - - - -
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Residues in contact with SER 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B LEU* 4.7 4.0 + - - +
130B PRO* 5.6 4.0 - - - -
131B TRP* 3.5 30.9 + - - -
134B MET* 3.7 23.7 - - - +
150B ASN* 3.4 8.1 - - - +
151B ALA* 3.5 3.9 + - - -
152B PHE* 2.9 28.8 + - - +
324B MET 3.0 8.7 + - - -
325B LEU* 2.8 21.6 + - - +
327B MET* 1.3 77.8 - - - +
329B PHE* 1.3 63.5 + - - +
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Residues in contact with PHE 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B LEU* 3.5 29.4 - - + -
150B ASN* 3.5 9.3 + - - -
152B PHE* 3.6 17.2 - - + +
160B LYS* 6.0 0.2 - - - +
161B VAL* 3.7 31.6 + - + +
171B PHE* 5.9 0.2 - + - -
175B PHE* 3.8 24.5 - + - -
325B LEU* 3.2 55.5 + - + -
328B SER* 1.3 83.5 + - - +
330B LEU* 1.3 99.7 + - + +
401B N7I 3.9 24.0 - + - -
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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