Contacts of the helix formed by residues 298 - 313 (chain A) in PDB entry 2POD
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 GLY 298 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ALA* 5.2 3.8 - - - +
81A MSE 3.8 14.3 - - - -
84A ASN* 5.0 4.4 - - - +
85A SER* 3.1 19.6 + - - -
88A ASP* 4.2 5.4 - - - +
296A TRP 3.5 0.8 + - - -
297A CYS* 1.3 78.9 - - - +
299A GLY* 1.3 62.5 + - - +
301A SER* 4.1 7.1 - - - -
302A GLU* 3.7 23.4 + - - +
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Residues in contact with GLY 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A SER* 3.5 17.5 - - - -
88A ASP* 3.4 9.4 - - - -
89A ILE* 5.0 0.4 - - - -
294A ILE* 3.1 25.7 + - - +
297A CYS* 3.8 1.9 - - - -
298A GLY* 1.3 77.5 - - - +
300A LEU* 1.3 65.8 + - - -
301A SER 3.1 1.6 - - - -
303A ALA* 3.1 23.4 + - - +
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Residues in contact with LEU 300 (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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88A ASP* 2.9 4.6 + - - -
89A ILE* 4.5 12.3 - - + +
92A TRP* 3.7 41.5 - - + +
103A ILE* 4.0 20.6 - - + -
107A LEU* 4.7 14.6 - - + -
294A ILE* 4.4 19.6 - - + +
299A GLY* 1.3 70.5 - - - -
301A SER* 1.3 54.8 + - - +
303A ALA* 4.2 3.4 - - - -
304A ARG* 2.7 39.4 + - - +
330A ALA* 3.7 33.9 - - + +
334A LEU* 4.1 19.7 - - + -
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Residues in contact with SER 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ILE* 3.3 21.1 - - - +
62A ASP* 3.9 5.5 + - - -
65A ALA* 4.1 15.8 - - - +
88A ASP* 3.0 28.8 + - - -
92A TRP* 3.7 1.8 - - - +
298A GLY 4.1 4.9 - - - -
299A GLY 3.1 0.2 - - - -
300A LEU* 1.3 78.3 - - - +
302A GLU* 1.3 63.7 + - - +
304A ARG* 3.3 31.6 + - - +
305A LYS* 3.3 20.2 - - - +
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Residues in contact with GLU 302 (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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65A ALA* 5.4 7.6 - - + +
274A THR* 3.6 15.6 - - + +
275A ARG* 2.9 63.6 + - - +
276A TRP* 4.1 5.5 - - - -
297A CYS 3.6 23.8 - - - +
298A GLY* 3.7 19.0 + - - +
299A GLY 3.5 2.4 + - - +
301A SER* 1.3 79.7 - - - +
303A ALA* 1.3 52.8 + - - +
305A LYS* 3.0 8.6 + - - +
306A ILE* 2.8 43.4 + - + +
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Residues in contact with ALA 303 (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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292A LEU* 3.7 29.1 - - + +
294A ILE* 3.9 14.8 - - + -
297A CYS* 3.9 4.2 - - - -
299A GLY 3.1 18.2 + - - +
300A LEU* 3.9 4.7 - - - +
302A GLU* 1.3 74.0 - - - +
304A ARG* 1.3 64.6 + - - +
306A ILE* 4.0 11.0 - - - +
307A ALA* 3.1 24.1 + - - +
334A LEU* 3.9 10.8 - - + +
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Residues in contact with ARG 304 (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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61A ILE* 4.8 0.6 - - - +
62A ASP* 2.9 38.4 + - - -
92A TRP* 3.5 35.6 - - - -
107A LEU* 3.7 26.5 - - + +
300A LEU 2.7 25.8 + - - +
301A SER* 3.3 25.0 + - - +
303A ALA* 1.3 72.1 - - - +
305A LYS* 1.3 78.7 + - + +
307A ALA* 3.5 4.7 + - - +
308A SER* 3.4 19.6 + - - -
334A LEU* 4.2 10.6 - - - +
337A ASN* 5.7 4.1 + - - +
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Residues in contact with LYS 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ASP* 3.1 24.9 + - - +
65A ALA* 6.1 1.8 - - - +
275A ARG* 3.6 51.9 - - - +
301A SER* 3.3 23.7 + - - +
302A GLU* 3.0 7.6 + - - +
304A ARG* 1.3 102.8 - - + +
306A ILE* 1.3 60.2 + - - +
308A SER* 3.1 9.7 + - - -
309A MSE 2.9 34.8 + - + +
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Residues in contact with ILE 306 (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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274A THR* 3.7 24.9 - - - +
275A ARG* 4.1 8.7 - - - +
278A PHE* 3.6 55.0 - - + -
282A LEU* 5.7 0.2 - - - +
290A VAL* 3.9 8.1 - - + -
292A LEU* 3.6 23.1 - - + -
297A CYS* 4.2 9.6 - - - -
302A GLU* 2.8 29.6 + - + +
303A ALA* 4.0 5.4 - - - +
305A LYS* 1.3 75.8 - - - +
307A ALA* 1.3 56.9 + - - +
309A MSE 3.3 8.8 + - + +
310A ALA* 2.9 28.4 + - - +
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Residues in contact with ALA 307 (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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292A LEU* 4.7 0.2 - - - +
303A ALA 3.1 19.4 + - - +
304A ARG 3.6 5.6 - - - +
305A LYS 3.3 0.2 - - - -
306A ILE* 1.3 76.7 - - - +
308A SER* 1.3 58.0 + - - +
310A ALA 3.5 0.2 + - - -
311A GLU 3.2 10.9 + - - -
317A VAL* 3.7 26.0 - - + +
334A LEU* 4.5 7.0 - - + -
338A ALA* 4.2 17.5 - - + -
340A ASN* 2.9 34.3 + - - +
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Residues in contact with SER 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ARG 3.4 10.3 + - - -
305A LYS* 3.1 16.2 + - - -
306A ILE 3.3 0.2 - - - -
307A ALA* 1.3 76.2 - - - +
309A MSE 1.3 64.9 + - - +
311A GLU* 3.7 14.9 + - - +
312A ALA* 3.7 15.1 + - - +
340A ASN* 5.1 0.2 - - - -
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Residues in contact with MSE 309 (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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275A ARG* 4.2 36.3 - - + +
278A PHE* 5.2 2.2 - - + -
279A ARG* 4.2 22.9 - - + -
282A LEU* 3.7 24.2 - - + -
305A LYS* 2.9 17.6 + - + +
306A ILE* 3.4 11.0 - - + +
308A SER* 1.3 73.5 + - - +
310A ALA* 1.3 66.8 + - - +
312A ALA* 2.9 15.9 + - - +
313A TRP* 3.2 38.1 - - + -
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Residues in contact with ALA 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A LEU* 4.3 12.7 - - + +
290A VAL* 3.7 28.9 - - + -
306A ILE 2.9 19.7 + - - +
307A ALA 3.6 6.3 - - - +
309A MSE 1.3 72.0 - - - +
311A GLU* 1.3 55.9 + - - +
313A TRP* 3.0 12.0 + - - -
315A LEU* 3.0 36.4 + - - +
317A VAL* 3.8 8.5 - - + -
340A ASN* 3.8 4.3 - - - +
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Residues in contact with GLU 311 (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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307A ALA 3.2 12.2 + - - +
308A SER* 3.7 17.2 - - - +
309A MSE 3.1 0.4 - - - -
310A ALA* 1.3 76.6 - - - +
312A ALA* 1.3 58.2 + - - +
313A TRP 3.1 0.2 - - - -
314A HIS* 3.0 24.9 + - - +
315A LEU 3.9 8.3 - - - +
339A PRO* 3.9 36.4 - - - +
340A ASN* 3.6 20.1 - - + +
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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
----------------------------------------------------------
308A SER 3.7 7.8 + - - +
309A MSE 2.9 13.4 + - - +
311A GLU* 1.3 77.6 - - - +
313A TRP* 1.3 73.1 + - + +
314A HIS* 3.3 13.5 + - - -
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Residues in contact with TRP 313 (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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282A LEU* 3.5 55.7 + - + -
283A GLU* 5.5 6.3 - - + +
285A ASN* 4.5 12.3 + - - -
309A MSE 3.2 52.3 - - + -
310A ALA 3.0 9.8 + - - +
312A ALA* 1.3 88.8 - - + +
314A HIS* 1.3 74.0 + - - +
315A LEU* 3.2 17.1 + - + +
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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