Contacts of the helix formed by residues 299 - 311 (chain A) in PDB entry 1IEQ
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 ASP 299 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A THR* 4.0 14.4 + - + +
297A GLY 2.8 2.2 + - - -
298A SER* 1.3 83.7 + - - +
300A TYR* 1.3 61.9 + - - +
301A SER* 3.5 10.9 + - - -
302A TYR* 3.0 39.2 + - + +
303A SER* 3.1 13.7 + - - -
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Residues in contact with TYR 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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289A ILE* 3.9 19.4 - - + +
290A ASP* 3.5 39.8 + - - -
297A GLY* 3.6 13.4 + - - +
299A ASP* 1.3 74.0 - - - +
301A SER* 1.3 62.8 + - - +
303A SER* 3.1 12.0 + - - -
304A VAL* 3.0 33.5 + - + +
317A VAL* 3.7 27.2 + - + +
320A LYS* 4.8 5.4 - - - +
323A GLN* 3.3 39.7 - - - +
324A PHE* 3.7 36.4 - - - +
327A ILE* 3.5 18.2 - - + -
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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
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299A ASP* 3.1 9.5 - - - -
300A TYR* 1.3 78.8 - - - +
302A TYR* 1.3 62.2 + - - +
304A VAL* 3.3 1.0 + - - +
305A LYS 3.1 7.8 + - - -
327A ILE* 3.9 21.4 - - - +
331A HIS* 3.1 42.5 + - - -
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Residues in contact with TYR 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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263A ALA* 5.1 4.0 - - - +
292A ILE* 3.9 24.5 - - + +
293A THR* 3.6 22.9 - - + -
299A ASP* 3.0 27.5 + - - +
301A SER* 1.3 76.5 + - - +
303A SER* 1.3 67.2 + - - +
305A LYS* 3.1 16.6 + - + +
306A ALA* 2.8 44.3 + - + +
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Residues in contact with SER 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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289A ILE* 2.9 43.2 + - - +
290A ASP* 3.8 9.7 + - - -
292A ILE* 4.1 5.6 - - - +
293A THR* 4.1 6.8 + - - +
297A GLY 5.2 0.5 + - - -
299A ASP 3.1 13.3 + - - -
300A TYR* 3.2 19.3 - - - -
302A TYR* 1.3 80.6 - - - +
304A VAL* 1.3 60.9 + - - +
306A ALA* 4.1 0.7 - - - +
307A SER* 2.8 31.6 + - - -
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Residues in contact with VAL 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ILE* 4.1 5.6 - - + -
300A TYR* 3.0 36.2 + - + +
301A SER 3.8 5.4 - - - +
303A SER* 1.3 74.6 - - - +
305A LYS* 1.3 64.0 + - - +
307A SER* 3.6 4.7 - - - -
308A ILE* 3.0 37.6 + - + +
324A PHE* 4.0 18.4 - - + -
327A ILE* 3.8 17.5 - - + -
328A LEU* 3.9 41.1 - - + -
331A HIS* 4.5 2.7 - - - +
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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
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301A SER 3.1 10.9 + - - +
302A TYR* 3.1 20.2 + - + +
304A VAL* 1.3 79.4 - - - +
306A ALA* 1.3 57.7 + - - +
308A ILE* 4.3 0.2 - - - +
309A LEU* 3.0 56.0 + - + +
331A HIS* 3.7 17.0 - - + +
336A VAL* 3.6 29.8 - - + +
337A ILE* 4.3 5.4 - - + -
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Residues in contact with ALA 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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262A HIS 4.2 1.8 - - - -
263A ALA* 4.1 19.5 - - + +
292A ILE* 4.4 4.0 - - + -
302A TYR* 2.8 47.5 + - + +
303A SER 4.1 2.0 - - - +
305A LYS* 1.3 75.8 - - - +
307A SER* 1.3 57.5 + - - +
309A LEU* 3.9 3.3 - - - +
310A ALA* 2.9 30.4 + - - +
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Residues in contact with SER 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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262A HIS 3.2 20.1 + - - -
289A ILE* 3.3 34.3 - - - +
292A ILE* 4.3 1.1 - - - +
303A SER 2.8 20.6 + - - -
304A VAL* 3.2 8.8 + - - -
306A ALA* 1.3 73.3 - - - +
308A ILE* 1.3 74.7 + - - +
310A ALA 3.2 6.6 + - - -
312A LEU* 3.2 33.7 + - - +
315A ILE* 4.3 3.8 - - - +
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Residues in contact with ILE 308 (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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32A MET* 3.7 30.7 - - + -
304A VAL* 3.0 32.5 + - + +
307A SER* 1.3 82.8 + - - +
309A LEU* 1.3 62.2 + - - +
311A GLY 3.1 3.5 + - - -
312A LEU 3.9 10.3 - - - +
313A ASP 5.2 0.2 - - - +
315A ILE* 4.2 25.6 - - + -
324A PHE* 4.8 0.2 - - + -
328A LEU* 4.3 11.4 - - + -
337A ILE* 3.8 23.6 - - + -
341A ARG* 2.7 51.7 + - + +
342A ILE* 4.6 1.3 - - + -
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Residues in contact with LEU 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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265A GLN* 3.2 26.9 + - - +
269A THR* 4.5 1.2 + - - -
305A LYS* 3.0 48.9 + - + +
306A ALA* 4.2 3.1 - - - +
308A ILE* 1.3 76.6 - - - +
310A ALA* 1.3 62.1 + - - +
311A GLY* 3.2 1.4 + - - -
336A VAL 4.1 21.3 - - - +
337A ILE* 4.1 12.8 - - + -
338A PRO* 4.1 20.2 - - + -
341A ARG* 4.5 10.5 - - + +
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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
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262A HIS 4.0 4.3 - - - +
263A ALA* 3.8 28.3 - - - +
264A ASN 4.1 2.5 - - - +
265A GLN* 3.4 27.7 - - - +
268A VAL* 3.5 11.0 - - + +
269A THR* 2.7 19.1 + - - -
306A ALA 2.9 20.4 + - - +
307A SER 3.4 7.2 - - - +
308A ILE 3.2 0.4 - - - -
309A LEU* 1.3 76.8 - - - +
311A GLY* 1.3 52.8 + - - +
312A LEU* 3.8 6.3 - - + -
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Residues in contact with GLY 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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268A VAL* 3.8 8.7 - - - +
269A THR* 3.2 13.7 - - - -
273A LYS* 2.7 31.7 + - - -
282A VAL* 4.5 0.2 - - - +
308A ILE 3.1 6.7 + - - -
309A LEU 3.1 4.4 - - - -
310A ALA* 1.3 80.4 - - - +
312A LEU* 1.3 68.1 + - - +
313A ASP* 3.0 1.4 + - - +
341A ARG* 3.4 10.9 + - - -
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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