Contacts of the helix formed by residues 313 - 325 (chain A) in PDB entry 5IWM
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 ASN 313 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311A ASP 3.8 2.8 + - - -
312A ALA* 1.3 70.7 - - - +
314A ALA* 1.3 61.4 + - - +
315A SER* 3.0 24.2 + - - -
316A VAL* 3.3 35.5 + - + +
317A ILE* 3.4 17.3 + - - +
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Residues in contact with ALA 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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249A ILE* 3.8 32.8 - - + +
257A GLN* 4.2 15.2 + - + +
259A ILE* 3.8 7.7 - - + +
308A VAL* 3.9 28.9 - - + -
312A ALA 3.1 5.6 + - - -
313A ASN* 1.3 70.2 + - - +
315A SER* 1.3 60.0 - - - +
316A VAL 3.3 0.2 - - - -
317A ILE* 3.5 4.2 + - - +
318A LEU* 3.1 26.2 + - - +
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Residues in contact with SER 315 (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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249A ILE* 3.3 20.8 - - - +
313A ASN* 3.0 11.3 + - - -
314A ALA* 1.3 75.1 - - - +
316A VAL* 1.3 60.5 + - - +
318A LEU* 3.5 6.9 + - - +
319A ASN* 3.0 37.8 + - - -
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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
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313A ASN* 3.3 36.5 + - + +
314A ALA 3.3 0.4 - - - -
315A SER* 1.3 75.4 - - - +
317A ILE* 1.3 61.3 + - + +
319A ASN* 3.4 9.3 + - + +
320A ASN* 3.0 48.1 + - - +
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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
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259A ILE* 4.2 8.5 - - + -
286A ILE* 4.3 6.5 - - + -
287A ASP 3.7 11.0 - - - +
288A GLY* 3.6 30.1 - - - +
289A ILE* 3.9 28.9 - - + -
308A VAL* 3.6 28.9 - - + -
312A ALA* 4.4 4.7 - - + -
313A ASN 3.4 13.3 + - - +
314A ALA 3.8 5.8 - - - +
315A SER 3.3 0.2 - - - -
316A VAL* 1.3 76.8 - - + +
318A LEU* 1.3 59.7 + - - +
320A ASN* 3.3 10.3 + - - +
321A LEU* 2.9 42.5 + - + +
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Residues in contact with LEU 318 (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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247A ALA* 3.9 26.9 - - + +
249A ILE* 4.6 20.2 - - + -
259A ILE* 4.0 18.1 - - + +
314A ALA 3.1 17.9 + - - +
315A SER* 3.6 7.2 - - - +
316A VAL 3.3 0.2 - - - -
317A ILE* 1.3 75.8 - - - +
319A ASN* 1.3 65.5 + - - +
321A LEU* 3.0 11.3 + - + +
322A TYR* 3.0 63.2 + - + +
327A LEU* 4.1 12.6 - - + -
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Residues in contact with ASN 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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244A ARG* 5.2 5.9 + - - -
315A SER* 3.0 25.3 + - - +
316A VAL* 3.6 9.2 - - + +
318A LEU* 1.3 77.5 - - - +
320A ASN* 1.3 63.9 + - - +
322A TYR* 3.2 29.0 + - - +
323A LYS* 3.3 26.7 + - - +
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Residues in contact with ASN 320 (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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286A ILE* 3.8 14.9 - - + +
287A ASP* 5.7 2.8 + - - -
316A VAL* 3.0 38.9 + - - +
317A ILE* 3.6 8.4 - - - +
319A ASN* 1.3 77.8 - - - +
321A LEU* 1.3 54.3 + - - +
323A LYS* 3.1 17.7 + - - +
324A GLN* 2.8 62.8 + - - +
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Residues in contact with LEU 321 (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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259A ILE* 4.2 10.5 - - + -
277A ILE* 4.0 27.6 - - + -
280A LEU* 5.4 1.3 - - + -
286A ILE* 3.8 19.7 - - + -
289A ILE* 4.0 6.3 - - + -
306A ILE* 3.7 28.5 - - + -
317A ILE* 2.9 36.2 + - + +
318A LEU* 3.0 10.3 + - + +
320A ASN* 1.3 76.7 - - - +
322A TYR* 1.3 56.0 + - - +
324A GLN* 4.5 0.7 - - - +
325A THR* 2.4 50.9 + - + +
327A LEU* 3.9 17.9 - - + -
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Residues in contact with TYR 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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244A ARG* 3.4 45.7 - - + +
245A SER* 3.8 14.7 + - - -
247A ALA* 3.9 8.7 + - + +
318A LEU* 3.0 55.0 + - + +
319A ASN* 3.5 19.5 - - - +
320A ASN 3.2 0.2 - - - -
321A LEU* 1.3 75.9 - - - +
323A LYS* 1.3 60.6 + - + +
325A THR 3.1 18.0 - - - +
327A LEU* 3.8 29.2 - - + -
328A GLN* 3.3 51.3 - - + +
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Residues in contact with LYS 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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319A ASN* 3.3 21.5 + - - +
320A ASN* 3.1 20.5 + - - +
322A TYR* 1.3 78.5 - - + +
324A GLN* 1.3 65.9 + - + +
325A THR 4.9 0.5 - - - +
328A GLN* 6.0 1.3 - - - +
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Residues in contact with GLN 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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276A LYS* 6.1 0.3 - - - +
280A LEU* 3.5 33.5 - - + +
285A LYS* 3.0 26.4 + - - +
286A ILE* 4.0 6.8 - - - +
320A ASN* 2.8 50.0 + - - +
321A LEU* 4.8 0.7 - - - -
323A LYS* 1.3 81.8 - - + +
325A THR* 1.3 62.7 + - + +
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Residues in contact with THR 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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276A LYS* 4.5 3.4 - - + +
277A ILE* 3.6 35.4 - - + +
280A LEU* 3.6 20.9 - - + -
321A LEU* 2.4 42.6 + - + +
322A TYR 3.1 17.0 - - - +
323A LYS 4.7 0.3 - - - +
324A GLN* 1.3 80.8 - - + +
326A PRO* 1.3 71.8 - - + +
327A LEU* 2.8 20.6 + - - +
328A GLN 3.5 4.9 + - - +
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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