Contacts of the helix formed by residues 313 - 329 (chain A) in PDB entry 4E70
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311A ASN 3.7 1.6 + - - -
312A ASP* 1.3 72.9 - - - +
314A ASN* 1.3 66.6 + - - +
316A MET* 3.4 2.4 + - - -
317A GLY* 2.9 24.3 + - - -
1076B HIS* 3.3 22.1 + - - -
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Residues in contact with ASN 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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312A ASP* 3.3 10.0 + - - +
313A SER* 1.3 86.8 + - - +
315A SER* 1.3 64.1 + - - +
317A GLY* 3.3 2.7 + - - -
318A THR* 3.1 26.4 + - - -
1018B HIS* 4.5 4.4 + - - -
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Residues in contact with SER 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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309A SER 4.6 2.1 + - - -
310A CYS* 3.4 21.1 - - - -
312A ASP* 2.7 35.0 + - - -
314A ASN* 1.3 75.0 - - - +
316A MET* 1.3 59.1 + - - +
318A THR* 3.2 4.8 + - - +
319A SER* 2.9 31.7 + - - -
360A LEU* 3.6 25.1 - - - +
1014B PRO* 6.2 0.7 - - - -
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Residues in contact with MET 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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305A LEU* 3.5 41.7 - - + +
306A ASP* 4.9 5.4 - - + -
310A CYS 3.5 11.6 + - - +
311A ASN* 4.5 11.4 - - + +
312A ASP 2.8 18.1 + - - +
313A SER* 3.9 3.8 - - - +
315A SER* 1.3 76.7 - - - +
317A GLY* 1.3 63.5 + - - +
319A SER* 3.2 2.6 + - - -
320A LEU* 2.9 51.3 + - + +
1072B ARG* 6.3 0.4 - - - -
1076B HIS* 4.0 11.9 - - + +
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Residues in contact with GLY 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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313A SER 2.9 13.8 + - - -
314A ASN* 3.7 2.2 - - - -
315A SER 3.3 0.2 - - - -
316A MET* 1.3 77.6 - - - +
318A THR* 1.3 56.4 + - - +
320A LEU* 3.4 2.7 + - - +
321A ILE* 3.0 31.9 + - - +
401A GOL 4.6 1.1 - - - -
1018B HIS* 4.2 13.0 - - - -
1073B MET* 5.1 0.9 - - - +
1076B HIS* 3.2 29.2 + - - -
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Residues in contact with THR 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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314A ASN 3.1 12.0 + - - -
315A SER* 3.7 7.9 - - - -
317A GLY* 1.3 72.7 - - - +
319A SER* 1.3 67.3 + - - +
321A ILE* 3.3 7.3 + - + +
322A LEU* 2.9 24.6 + - + +
360A LEU* 3.8 19.3 - - + -
1014B PRO* 3.6 26.3 + - + +
1017B TRP* 4.3 11.4 - - + -
1018B HIS* 2.9 36.2 + - + +
1021B LEU* 5.9 0.2 - - + -
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Residues in contact with SER 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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303A HIS* 4.7 0.9 + - - -
305A LEU* 3.5 26.6 - - - +
310A CYS* 4.5 10.7 + - - +
315A SER 2.9 20.4 + - - -
316A MET* 3.5 7.1 - - - -
318A THR* 1.3 76.4 - - - +
320A LEU* 1.3 60.0 + - - +
322A LEU* 3.2 2.1 + - - -
323A ASP* 2.8 24.4 + - - +
334A LEU* 3.4 22.4 - - - +
360A LEU* 3.9 21.4 - - - +
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Residues in contact with LEU 320 (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 LEU* 4.2 12.1 - - + -
316A MET* 2.9 41.6 + - + +
317A GLY* 3.9 3.8 - - - +
319A SER* 1.3 73.9 - - - +
321A ILE* 1.3 60.3 + - - +
323A ASP* 3.2 9.1 + - + +
324A MET* 2.9 32.9 + - - +
1069B ARG 5.9 0.2 - - - +
1072B ARG* 3.6 48.7 - - + +
1073B MET* 4.1 17.9 - - - +
1076B HIS* 3.5 33.7 - - + -
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Residues in contact with ILE 321 (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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317A GLY 3.0 15.8 + - - +
318A THR* 3.6 6.3 - - + +
320A LEU* 1.3 76.3 - - - +
322A LEU* 1.3 57.2 + - - +
324A MET* 3.2 4.4 + - - +
325A LEU* 2.9 26.5 + - - +
401A GOL 5.4 0.7 - - - +
1017B TRP 5.3 0.4 - - - +
1018B HIS* 3.5 43.7 - - + +
1021B LEU* 3.4 46.9 - - + +
1024B ILE* 4.1 13.4 - - + +
1025B ASN* 3.8 18.4 - - - +
1073B MET* 3.8 20.6 - - + -
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Residues in contact with LEU 322 (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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268A TRP* 5.1 2.0 - - + -
303A HIS* 3.7 31.2 - - + +
318A THR* 2.9 20.2 + - + +
319A SER* 3.5 7.9 - - - +
321A ILE* 1.3 72.5 - - - +
323A ASP* 1.3 61.3 + - - +
325A LEU* 3.1 7.1 + - + -
326A PHE* 2.8 39.3 + - + -
334A LEU* 4.0 11.7 - - + -
360A LEU* 4.0 6.7 - - + -
403A N7I 3.7 33.2 - - + -
1017B TRP* 4.0 26.0 - - + -
1021B LEU* 3.8 19.3 - - + -
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Residues in contact with ASP 323 (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 LEU* 5.9 0.4 - - + -
319A SER 2.8 14.4 + - - +
320A LEU* 3.2 16.4 + - + +
322A LEU* 1.3 75.2 - - - +
324A MET* 1.3 61.2 + - + +
326A PHE* 3.6 1.4 + - - +
327A MET* 3.0 22.5 + - - +
333A SER* 3.4 3.8 - - - -
334A LEU* 2.9 39.0 + - + +
1069B ARG* 3.0 52.1 + - - +
1072B ARG* 3.2 25.2 + - - +
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Residues in contact with MET 324 (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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131A TRP* 3.3 16.7 - - + -
320A LEU 2.9 17.8 + - - +
321A ILE 3.5 7.2 - - - +
323A ASP* 1.3 81.8 - - - +
325A LEU* 1.3 66.9 + - - +
327A MET* 3.2 25.0 + - + +
328A SER 3.0 18.2 + - - -
1024B ILE* 3.6 17.7 - - + -
1028B THR* 3.9 24.0 - - + -
1069B ARG* 3.4 42.6 - - + +
1070B LEU* 3.7 17.5 - - - +
1073B MET* 4.0 15.0 - - + -
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Residues in contact with LEU 325 (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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127A LEU* 4.4 12.8 - - + +
131A TRP* 5.6 0.4 - - - +
321A ILE 2.9 14.0 + - - +
322A LEU* 3.1 9.6 + - + +
324A MET* 1.3 74.5 - - - +
326A PHE* 1.3 74.4 + - + +
328A SER* 2.8 27.2 + - - +
329A PHE* 3.1 30.4 + - + -
403A N7I 3.6 44.2 - - + +
1021B LEU* 4.1 18.4 - - + -
1023B TYR* 3.9 21.3 - - - +
1024B ILE* 4.1 12.0 - - + +
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Residues in contact with PHE 326 (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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268A TRP* 4.5 8.3 - - - -
271A CYS* 3.8 37.7 - - + -
272A ASP* 4.7 0.7 - - - -
303A HIS* 5.0 1.6 - + - -
322A LEU* 2.8 29.5 + - + +
323A ASP 3.9 3.8 - - - +
325A LEU* 1.3 85.1 - - + +
327A MET* 1.3 64.8 + - - +
329A PHE* 4.5 0.2 - + - -
330A LEU* 2.9 50.2 + - + +
332A GLY 4.0 15.2 - - - +
333A SER* 4.5 3.1 - - - +
334A LEU* 3.6 28.9 - - + -
403A N7I 3.7 50.9 - + + -
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Residues in contact with MET 327 (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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131A TRP* 4.6 3.1 - - + -
134A MET* 4.1 29.6 - - + +
137A TRP* 4.9 7.8 - - + -
138A LEU* 5.2 3.4 - - + -
150A ASN* 3.7 16.1 - - - +
151A ALA 4.7 0.7 + - - -
323A ASP 3.0 13.1 + - - +
324A MET* 3.2 34.1 + - + +
326A PHE* 1.3 78.2 - - - +
328A SER* 1.3 60.0 + - - +
330A LEU 4.0 2.0 - - - +
332A GLY 4.3 2.0 - - - -
1066B PHE* 3.7 61.5 - - + +
1069B ARG* 3.4 23.0 - - - +
1070B LEU* 4.7 7.4 - - + -
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Residues in contact with SER 328 (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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127A LEU* 4.7 4.6 + - - +
130A PRO* 5.6 3.8 - - - -
131A TRP* 3.4 37.4 + - - -
134A MET* 3.7 15.3 - - - -
150A ASN* 3.4 7.6 - - - +
151A ALA* 3.6 3.3 + - - -
152A PHE* 3.0 28.5 + - - +
324A MET 3.0 9.9 + - - -
325A LEU* 2.8 21.3 + - - +
327A MET* 1.3 79.3 - - - +
329A PHE* 1.3 64.0 + - - +
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Residues in contact with PHE 329 (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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127A LEU* 3.6 26.5 - - + -
150A ASN* 3.4 11.0 + - - -
152A PHE* 3.7 16.4 - - + +
161A VAL* 3.7 35.5 + - + +
171A PHE* 5.8 0.9 - + - -
175A PHE* 3.8 23.6 - + - -
325A LEU* 3.1 55.7 + - + -
326A PHE* 4.5 0.4 - + - -
328A SER* 1.3 83.6 + - - +
330A LEU* 1.3 99.7 + - + +
403A N7I 3.8 22.9 - + - -
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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
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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