Contacts of the helix formed by residues 297 - 311 (chain A) in PDB entry 3AE1
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 297 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A GLY* 4.7 1.6 - - - -
132A GLY 5.0 1.8 - - - -
133A GLY* 4.5 5.6 - - - -
296A ALA* 1.3 81.0 - - - +
298A ARG* 1.3 63.7 + - - +
299A ASP* 3.2 20.9 - - - -
300A VAL* 3.3 16.4 + - - -
301A VAL* 3.1 22.2 + - - +
408A ASN* 4.0 4.5 + - - -
410A LEU* 5.1 4.4 - - - +
620A ARG* 3.4 10.4 + - - -
622A TYR* 2.9 35.2 + - - -
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Residues in contact with ARG 298 (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 PHE* 3.9 1.2 - - - -
132A GLY 5.5 1.7 + - - +
252A GLN* 3.1 35.9 + - - +
253A PHE 3.7 3.4 - - - +
254A HIS* 3.3 22.3 + - - -
255A PRO* 3.6 25.8 - - + +
267A GLU* 3.1 34.1 + - - +
296A ALA 4.5 0.4 - - - -
297A SER* 1.3 73.8 - - - +
299A ASP* 1.3 59.1 + - - +
301A VAL* 5.0 0.2 - - - -
302A SER* 2.9 28.1 + - - -
365A HIS* 3.3 7.7 + - - -
408A ASN* 3.8 5.9 + - - +
409A ARG* 3.0 33.2 - - - +
410A LEU* 5.4 0.9 - - - +
411A GLY* 3.4 20.7 - - - +
701A MLI 2.8 43.4 + - - -
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Residues in contact with ASP 299 (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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252A GLN* 5.3 1.1 - - - +
253A PHE 5.2 1.3 - - - +
297A SER* 3.2 13.9 - - - -
298A ARG* 1.3 75.7 - - - +
300A VAL* 1.3 62.0 + - - +
302A SER* 3.5 6.7 + - - -
303A ARG* 2.8 54.8 + - - +
408A ASN* 3.2 19.4 - - - +
483A VAL* 5.4 0.3 - - - +
548A GLY* 3.0 24.9 - - - +
549A ALA* 3.8 9.2 - - + +
620A ARG* 2.8 32.3 + - - -
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Residues in contact with VAL 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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285A MET* 5.1 2.5 - - + -
288A TYR* 5.7 6.1 - - + +
289A ALA* 5.4 9.0 - - + -
296A ALA* 5.1 8.3 - - + -
297A SER* 3.3 27.0 + - - +
299A ASP* 1.3 89.5 - - - +
301A VAL* 1.3 57.8 + - - +
303A ARG* 3.4 12.1 - - + +
304A SER* 2.7 36.5 + - - +
620A ARG* 4.1 8.7 - - - +
621A SER* 6.3 1.3 - - - -
622A TYR* 4.8 12.3 - - + +
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Residues in contact with VAL 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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255A PRO* 3.7 25.4 - - + -
270A ARG* 3.9 14.6 - - - +
276A LEU* 3.8 23.1 - - + -
285A MET* 3.7 30.5 - - + -
294A ASP 4.2 7.0 - - - +
296A ALA* 3.9 20.2 - - + +
297A SER 3.1 18.0 + - - +
300A VAL* 1.3 75.9 - - - +
302A SER* 1.3 57.1 + - - +
304A SER* 3.1 6.8 + - - -
305A MET* 3.0 29.0 + - - +
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Residues in contact with SER 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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253A PHE* 3.1 30.4 + - - +
255A PRO* 3.9 6.5 - - - -
298A ARG 2.9 19.0 + - - -
299A ASP* 3.5 8.7 + - - -
301A VAL* 1.3 76.3 - - - +
303A ARG* 1.3 57.5 + - - +
305A MET* 3.7 13.1 - - - +
306A THR* 2.7 36.4 + - - -
362A PRO* 3.7 18.7 - - - +
483A VAL* 4.2 5.8 - - - +
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Residues in contact with ARG 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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299A ASP* 2.8 49.7 + - - +
300A VAL* 3.4 14.2 - - + +
301A VAL 3.2 0.4 - - - -
302A SER* 1.3 78.2 - - - +
304A SER* 1.3 58.0 + - - +
306A THR 3.6 0.7 + - - -
307A LEU* 3.1 29.7 + - + +
483A VAL* 3.9 18.9 - - - +
484A PHE* 3.4 38.0 - - + -
546A SER* 5.7 4.0 - - - -
548A GLY* 2.9 18.7 + - - +
549A ALA 5.1 2.4 + - - -
551A ALA* 3.8 22.6 - - - +
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Residues in contact with SER 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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284A PHE* 3.9 3.4 - - - -
285A MET* 3.7 14.6 - - - +
288A TYR* 3.3 54.1 + - - +
300A VAL* 2.7 21.1 + - - +
301A VAL 3.1 7.8 + - - -
303A ARG* 1.3 75.9 - - - +
305A MET* 1.3 59.8 + - - +
307A LEU* 3.3 2.5 + - - +
308A GLU* 3.0 33.6 + - - +
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Residues in contact with MET 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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255A PRO* 3.2 51.6 - - - +
256A THR* 4.8 0.2 - - + -
276A LEU* 3.6 20.6 - - + -
284A PHE* 3.9 21.8 - - + -
301A VAL 3.0 16.4 + - - +
302A SER* 3.7 7.4 - - - +
303A ARG 3.3 0.2 - - - -
304A SER* 1.3 76.1 - - - +
306A THR* 1.3 62.6 + - - +
308A GLU* 3.2 13.3 + - - +
309A ILE* 3.2 20.4 + - - +
322A VAL* 3.8 28.1 - - + +
360A VAL* 3.8 17.9 - - + +
362A PRO* 4.0 17.9 - - + -
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Residues in contact with THR 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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302A SER 2.7 21.7 + - - -
303A ARG 4.0 4.0 - - - -
304A SER 3.4 0.2 - - - -
305A MET* 1.3 77.0 - - - +
307A LEU* 1.3 56.6 + - - +
309A ILE* 3.6 15.6 + - + +
310A ARG* 3.1 34.2 + - + +
362A PRO* 3.5 10.1 - - + +
483A VAL* 3.5 29.7 - - + +
484A PHE* 4.2 17.3 - - + +
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Residues in contact with LEU 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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288A TYR* 3.6 31.2 - - + +
303A ARG* 3.1 16.7 + - + +
304A SER* 3.6 5.8 - - - +
305A MET 3.1 0.2 - - - -
306A THR* 1.3 77.6 - - - +
308A GLU* 1.3 63.3 + - - +
310A ARG* 3.4 21.7 - - - +
311A GLU* 3.3 45.7 + - - +
484A PHE* 3.8 27.8 - - + -
553A GLU* 5.9 1.1 - - - +
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Residues in contact with GLU 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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278A ASN* 3.0 27.2 + - + +
284A PHE* 3.8 20.3 - - + +
287A ARG* 3.2 23.6 + - - -
288A TYR* 3.2 20.8 + - - +
304A SER 3.0 20.6 + - - +
305A MET* 3.2 6.3 + - - +
307A LEU* 1.3 74.3 - - - +
309A ILE* 1.3 61.3 + - - +
311A GLU 3.5 4.9 + - - -
313A ARG* 3.0 70.9 + - - +
322A VAL* 4.9 7.2 - - + -
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Residues in contact with ILE 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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305A MET 3.2 19.2 + - - +
306A THR* 3.7 17.3 - - + +
308A GLU* 1.3 74.3 - - - +
310A ARG* 1.3 66.0 + - - +
311A GLU 3.1 0.9 + - - -
312A GLY* 3.2 12.6 + - - -
313A ARG 4.5 6.5 - - - +
314A GLY* 4.9 1.6 - - - +
319A LYS 4.2 7.3 - - - +
320A ASP* 3.6 46.2 - - + +
321A HIS* 4.4 11.7 - - - +
322A VAL* 4.6 6.3 - - + +
361A LEU* 3.7 19.5 - - + -
362A PRO* 4.9 4.0 - - + -
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Residues in contact with ARG 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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306A THR* 3.1 22.0 + - + +
307A LEU* 3.4 28.1 - - + +
309A ILE* 1.3 79.5 - - - +
311A GLU* 1.3 62.9 + - + +
312A GLY 3.4 2.8 + - - -
484A PHE* 3.5 40.6 + - - +
553A GLU* 3.5 17.7 + - - +
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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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288A TYR* 4.7 4.8 + - - -
307A LEU* 3.3 41.2 + - - +
308A GLU 3.5 0.4 + - - -
309A ILE 3.1 1.6 - - - -
310A ARG* 1.3 80.9 - - + +
312A GLY* 1.3 56.1 + - - +
313A ARG* 3.2 46.1 + - - +
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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