Contacts of the helix formed by residues 310 - 327 (chain A) in PDB entry 3REO
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 310 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A ASP* 2.8 22.2 + - - -
309A PRO* 1.3 83.3 - - - +
311A ILE* 1.3 65.4 + - - +
312A ALA* 3.7 7.0 + - - +
313A THR* 3.1 19.1 + - - -
314A LYS* 3.0 20.6 + - - +
305B PRO* 4.2 19.1 - - - -
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Residues in contact with ILE 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A PRO 3.6 2.9 + - - +
310A SER* 1.3 72.4 - - - +
312A ALA* 1.3 58.7 + - - +
314A LYS* 3.2 9.0 + - + +
315A VAL* 2.9 29.1 + - - +
20C GLU* 4.9 7.0 - - + +
23C LEU* 3.6 38.4 - - + +
24C PHE* 3.7 22.7 - - + +
27C GLN* 3.8 26.7 - - + +
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Residues in contact with ALA 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A PRO* 5.5 0.2 - - - -
310A SER* 3.1 7.0 + - - +
311A ILE* 1.3 78.8 - - - +
313A THR* 1.3 63.4 + - - +
315A VAL* 3.3 6.9 + - - -
316A VAL* 3.3 6.4 + - - +
358A ASN* 3.0 36.5 + - - +
23C LEU* 3.6 25.3 - - + +
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Residues in contact with THR 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A PRO* 3.5 25.7 - - + +
306A SER 3.8 5.2 - - - +
308A ASP* 2.7 46.6 + - - +
310A SER* 3.1 18.8 + - - -
312A ALA* 1.3 78.0 - - - +
314A LYS* 1.4 62.0 + - - +
316A VAL* 3.0 4.7 + - - +
317A ILE* 2.9 44.8 + - + +
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Residues in contact with LYS 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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308A ASP 4.3 2.0 - - - +
309A PRO* 3.0 31.0 + - - +
310A SER 3.0 13.3 + - - +
311A ILE* 3.5 10.1 - - + +
313A THR* 1.4 73.7 - - - +
315A VAL* 1.3 59.2 + - - +
317A ILE* 4.5 5.2 - - - +
318A HIS* 2.7 40.1 + - - +
27C GLN* 3.6 24.9 - - + +
89C SER* 3.3 42.3 + - - +
90C TYR* 3.6 39.8 - - + +
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Residues in contact with VAL 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A TYR* 3.6 26.0 - - + +
311A ILE 2.9 20.6 + - - +
312A ALA 3.7 5.4 - - - +
313A THR 3.2 0.4 - - - -
314A LYS* 1.3 77.0 - - - +
316A VAL* 1.3 60.2 + - - +
318A HIS* 3.5 7.2 + - - +
319A THR* 2.9 30.2 + - - +
358A ASN* 3.7 12.1 - - - +
23C LEU* 3.2 35.9 - - + +
26C MET* 3.9 15.5 - - + -
27C GLN* 3.7 17.9 - - + +
30C SER* 5.8 0.9 - - - +
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Residues in contact with VAL 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A TYR* 3.8 35.4 - - + -
302A ILE 3.9 20.0 - - - +
303A LEU* 3.9 16.6 - - + -
304A PRO* 4.2 10.3 - - + -
312A ALA 3.5 5.6 - - - +
313A THR* 3.0 7.0 + - - +
315A VAL* 1.3 75.1 - - - +
317A ILE* 1.3 58.1 - - - +
319A THR* 3.2 1.7 + - - -
320A ASP* 2.9 23.4 + - - +
332A GLU* 3.6 19.2 - - + +
358A ASN* 3.4 29.2 - - - +
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Residues in contact with ILE 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A LEU* 4.8 8.3 - - + -
304A PRO* 5.1 2.9 - - + -
306A SER 4.5 1.3 - - - +
307A PRO* 3.9 13.9 - - + -
313A THR* 2.9 40.5 + - + +
314A LYS* 4.0 4.7 - - - +
316A VAL* 1.3 75.9 - - + +
318A HIS* 1.4 64.2 + - - +
320A ASP* 3.2 9.1 + - + +
321A ALA* 2.9 22.3 + - - +
82C ARG 5.0 1.7 - - - +
85C ARG* 3.8 33.7 - - + +
86C LEU* 3.3 42.4 - - + +
89C SER* 4.1 11.4 - - - +
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Residues in contact with HIS 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A LYS* 2.7 30.6 + - - +
315A VAL* 3.6 5.2 - - - +
317A ILE* 1.4 74.1 - - - +
319A THR* 1.3 57.9 + - - +
321A ALA* 3.1 7.7 + - - +
322A LEU* 2.9 31.3 + - - +
27C GLN* 3.5 32.8 + - + +
30C SER* 2.8 42.2 + - - +
31C ALA* 4.0 9.2 + - + -
33C VAL* 4.3 7.2 - - + +
34C LEU* 5.6 1.6 - - - +
86C LEU* 3.8 20.8 - - + +
90C TYR* 2.7 34.2 + + - -
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Residues in contact with THR 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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269A TRP* 5.3 6.1 - - + -
272A HIS* 3.6 20.9 - - + -
301A TYR* 3.3 22.9 + - + -
315A VAL* 2.9 19.1 + - - +
316A VAL 3.2 4.7 + - - -
318A HIS* 1.3 75.2 - - - +
320A ASP* 1.3 66.2 + - - +
322A LEU* 3.3 14.8 + - + +
323A MET* 2.9 32.1 + - - +
332A GLU* 3.0 25.8 - - - +
26C MET* 5.8 1.4 - - - +
30C SER* 5.6 0.3 + - - -
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Residues in contact with ASP 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A LEU* 5.0 1.6 - - + -
316A VAL 2.9 14.6 + - - +
317A ILE* 3.2 13.3 + - - +
319A THR* 1.3 79.3 - - - +
321A ALA* 1.4 60.8 + - - +
323A MET* 3.5 3.6 + - - +
324A LEU* 3.2 6.4 + - - +
331A LYS* 3.4 2.9 - - - +
332A GLU* 2.9 38.8 + - + +
82C ARG* 2.8 61.9 + - - +
85C ARG* 3.0 32.2 + - - +
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Residues in contact with ALA 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TRP* 3.7 14.2 - - + -
317A ILE 2.9 12.7 + - - +
318A HIS 3.1 4.0 + - - +
320A ASP* 1.4 77.0 + - - +
322A LEU* 1.3 64.4 + - - +
324A LEU* 3.2 16.1 + - + +
325A ALA* 3.1 16.6 + - - +
33C VAL* 3.4 28.3 - - + -
37C ALA* 5.6 1.1 - - + -
82C ARG* 5.2 6.3 - - - +
83C VAL* 6.0 2.5 - - + -
86C LEU* 3.8 15.9 - - + -
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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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130A PHE* 5.4 10.8 - - + -
134A ALA* 5.3 13.0 - - + +
143A TRP* 4.0 6.1 - - + +
318A HIS 2.9 16.7 + - - +
319A THR* 3.5 19.7 - - + +
321A ALA* 1.3 76.8 - - - +
323A MET* 1.3 61.9 + - + +
325A ALA 3.0 2.3 + - - -
326A TYR* 2.9 70.1 + - + +
30C SER* 4.1 20.4 - - - -
33C VAL* 3.4 24.7 - - + -
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Residues in contact with MET 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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272A HIS* 3.2 45.3 - - + +
273A ASP* 3.6 13.7 - - - +
319A THR* 2.9 31.2 + - - +
320A ASP 3.5 6.3 - - - +
322A LEU* 1.3 75.8 - - + +
324A LEU* 1.3 58.0 + - - +
326A TYR* 5.5 0.9 - - + -
327A ASN* 2.8 72.9 + - + +
329A GLY 5.0 0.2 - - - -
330A GLY* 3.4 23.7 - - - +
331A LYS* 4.0 6.1 - - - +
332A GLU* 3.8 9.4 - - - +
82C ARG* 3.8 0.2 - - - +
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Residues in contact with LEU 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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143A TRP* 6.3 0.9 - - + -
146A LEU* 4.2 19.5 - - + -
155A ILE* 4.6 3.1 - - - +
156A PRO* 3.3 18.7 - - - +
320A ASP 3.2 4.9 + - - +
321A ALA* 3.2 16.9 + - + +
323A MET* 1.3 80.1 - - - +
325A ALA* 1.3 59.9 + - - +
326A TYR 3.7 0.3 + - - -
327A ASN 4.7 1.6 - - - +
329A GLY* 6.5 0.2 - - - -
330A GLY 4.7 0.2 - - - -
79C MET* 3.9 53.2 - - + +
82C ARG* 3.5 40.1 - - + +
83C VAL* 4.1 16.6 - - + +
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Residues in contact with ALA 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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142A PRO* 3.4 19.0 - - + +
143A TRP* 3.6 47.8 - - + -
146A LEU* 5.7 2.0 - - + -
156A PRO* 4.1 16.2 - - + -
157A PHE 3.6 6.9 + - - -
321A ALA 3.1 4.1 + - - +
322A LEU 3.0 3.2 + - - +
324A LEU* 1.3 76.4 - - + +
326A TYR* 1.3 79.5 + - + +
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Residues in contact with TYR 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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134A ALA* 4.8 5.5 + - - -
139A LEU* 2.9 60.7 + - + +
140A LEU* 5.7 0.3 - - - +
142A PRO* 3.9 14.8 - - + -
143A TRP* 3.0 23.3 + - - -
155A ILE* 4.0 6.9 - - - +
157A PHE* 3.6 15.4 - + + +
158A ASN* 4.8 0.9 + - - -
165A ILE* 3.5 30.6 + - + +
322A LEU* 2.9 45.3 + - + +
323A MET* 5.5 1.1 - - + -
324A LEU 3.4 0.2 - - - -
325A ALA* 1.3 106.8 - - + +
327A ASN* 1.3 78.8 + - - +
328A PRO* 4.3 0.3 - - - +
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Residues in contact with ASN 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ILE* 3.6 15.7 - - - +
158A ASN* 5.9 0.2 - - - -
165A ILE* 3.5 20.1 - - - +
166A PHE* 3.5 16.5 - - - -
273A ASP* 3.4 16.5 + - - +
323A MET* 2.8 51.6 + - + +
324A LEU* 4.7 1.7 - - - +
326A TYR* 1.3 98.6 - - - +
328A PRO* 1.3 64.6 - - + +
329A GLY* 2.4 20.9 + - - -
330A GLY 4.1 2.9 - - - +
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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
------------------------------------------------------------
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