Contacts of the helix formed by residues 303 - 314 (chain A) in PDB entry 1ECX
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 ARG 303 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A ASN 4.4 0.2 - - - -
302A ILE* 1.3 72.7 - - - +
304A GLY* 1.3 66.5 + - - +
305A SER* 4.1 14.0 + - - +
306A THR* 2.9 30.4 + - - +
307A LEU* 3.0 11.6 + - - +
346A GLN* 3.2 51.5 + - + +
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Residues in contact with GLY 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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302A ILE 3.4 2.4 + - - -
303A ARG* 1.3 69.9 - - - +
305A SER* 1.3 51.7 + - - +
307A LEU* 3.0 5.0 + - - +
308A GLN* 2.6 36.4 + - - +
320A THR* 3.3 8.4 - - - +
346A GLN 2.9 15.2 + - - -
347A GLY* 3.4 21.2 - - - -
348A ALA 3.9 5.4 - - - -
349A ILE* 3.5 12.2 - - - +
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Residues in contact with SER 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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303A ARG* 4.1 13.2 + - - +
304A GLY* 1.3 75.0 - - - +
306A THR* 1.3 63.1 + - - +
308A GLN* 3.2 9.3 + - - +
309A ASN* 2.8 37.1 + - - +
320A THR* 3.5 17.5 - - - +
346A GLN 4.9 0.2 + - - -
278B ASN* 4.5 16.8 + - - -
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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 ILE* 4.6 2.5 - - + -
303A ARG* 2.9 29.1 + - - +
305A SER* 1.3 77.3 + - - +
307A LEU* 1.3 67.8 + - - +
309A ASN* 3.1 2.1 + - - +
310A LEU* 3.0 41.1 + - + +
376A LEU* 4.3 20.2 - - + -
274B SER* 3.5 27.3 + - - +
278B ASN* 5.2 2.1 + - - -
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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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299A PHE* 3.7 31.2 - - + -
302A ILE* 4.1 19.0 - - + +
303A ARG 3.0 11.0 + - - +
304A GLY* 3.4 9.2 - - - +
306A THR* 1.3 77.6 - - - +
308A GLN* 1.3 62.8 + - - +
310A LEU* 3.5 2.8 + - - +
311A LEU* 3.0 40.7 + - + +
347A GLY 5.1 2.9 - - - +
349A ILE* 3.7 32.3 - - + -
369A ILE* 4.2 15.7 - - + -
372A ILE* 4.2 16.4 - - + -
373A LEU* 5.0 6.1 - - + -
376A LEU* 5.0 2.7 - - + -
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Residues in contact with GLN 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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304A GLY 2.6 19.4 + - - +
305A SER* 3.3 11.4 + - - +
307A LEU* 1.3 73.6 - - - +
309A ASN* 1.3 67.5 + - - +
311A LEU* 3.3 2.5 + - - +
312A SER* 2.9 27.6 + - - -
316A ILE 4.8 0.3 - - - +
318A VAL* 2.9 40.8 - - + +
319A SER* 3.7 7.6 - - - -
320A THR* 3.1 34.2 + - + +
349A ILE* 4.6 0.6 - - - +
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Residues in contact with ASN 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 SER* 2.8 30.1 + - - +
306A THR 3.1 4.5 + - - +
308A GLN* 1.3 78.9 + - - +
310A LEU* 1.3 63.2 + - - +
312A SER* 3.2 3.6 + - - -
313A GLY* 3.1 12.3 + - - -
274B SER* 3.2 31.9 + - - -
277B MET* 2.7 53.4 - - + +
278B ASN* 3.0 27.0 + - - +
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Residues in contact with LEU 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* 3.0 46.8 + - + +
307A LEU* 4.0 1.6 - - - +
309A ASN* 1.3 73.3 - - + +
311A LEU* 1.3 67.5 + - - +
313A GLY* 2.8 12.7 + - - +
314A TYR* 3.1 21.0 - - + -
372A ILE* 3.6 35.0 - - + -
375A PHE* 6.1 1.8 - - + -
376A LEU* 4.5 8.7 - - + -
270B SER* 3.7 36.3 - - - +
273B VAL* 4.2 11.9 - - + -
274B SER* 4.0 15.5 - - - -
287B LEU* 4.4 11.9 - - + -
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Residues in contact with LEU 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 LEU* 3.0 38.3 + - + +
308A GLN* 3.7 3.8 - - - +
310A LEU* 1.3 76.5 - - - +
312A SER* 1.3 62.9 + - - +
314A TYR* 3.0 9.9 + - - +
315A GLY 3.4 0.2 + - - -
316A ILE* 3.0 56.0 + - + +
318A VAL* 4.1 23.3 - - + -
349A ILE* 4.2 13.0 - - + -
365A PHE* 4.3 11.4 - - + -
369A ILE* 4.2 25.1 - - + -
372A ILE* 3.7 19.3 - - + -
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Residues in contact with SER 312 (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 GLN* 2.9 16.9 + - - -
309A ASN* 3.4 11.9 - - - -
311A LEU* 1.3 76.4 - - - +
313A GLY* 1.3 59.3 + - - +
315A GLY* 2.9 19.4 + - - -
316A ILE 3.1 14.1 + - - -
317A TYR* 3.7 22.4 + - - -
124B ARG* 5.2 1.9 + - - -
277B MET* 4.6 10.8 - - - -
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Residues in contact with GLY 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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309A ASN 3.1 9.0 + - - -
310A LEU 2.8 9.9 + - - -
312A SER* 1.3 75.8 - - - +
314A TYR* 1.3 56.7 + - - +
315A GLY 3.3 1.0 + - - -
124B ARG* 3.8 7.0 + - - -
273B VAL* 5.4 0.2 - - - -
277B MET* 4.7 4.2 - - - +
283B ILE* 5.1 12.1 - - - -
285B THR 4.1 3.3 - - - +
287B LEU* 3.2 46.1 + - - +
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Residues in contact with TYR 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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1A MET 3.8 1.9 - - - +
310A LEU* 3.1 24.7 - - + -
311A LEU* 3.0 9.8 + - - +
313A GLY* 1.3 75.0 - - - +
315A GLY* 1.3 61.1 + - - +
316A ILE* 3.4 13.9 - - + -
364A TYR* 3.0 24.9 + - - +
368A LYS* 3.9 19.3 - - + -
371A GLU* 4.2 17.5 + - - -
372A ILE* 3.6 26.4 - - + +
375A PHE* 3.5 28.8 - + - -
124B ARG* 3.5 7.3 + - - -
266B GLU* 4.5 8.5 + - - -
287B LEU* 3.6 28.6 + - + +
288B GLU* 3.6 37.4 - - + +
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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