Contacts of the helix formed by residues 319 - 331 (chain A) in PDB entry 5ICN
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 319 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311A GLN* 4.1 0.4 - - - +
317A TRP 4.2 0.8 + - - -
318A LYS* 1.3 74.5 - - - +
320A LEU* 1.3 68.5 + - - +
321A THR* 4.4 9.1 + - - -
322A SER* 2.6 40.9 + - - -
323A ILE* 3.2 4.4 + - - +
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Residues in contact with LEU 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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307A PHE* 3.4 44.6 - - + +
308A THR* 3.9 18.6 - - + +
311A GLN* 3.4 21.8 + - - +
319A SER* 1.3 70.0 - - - +
321A THR* 1.3 62.7 + - + +
323A ILE* 2.9 27.2 + - + +
324A ILE* 3.0 22.7 + - + +
23B TYR* 6.0 4.0 - - + -
104B ASP* 3.8 38.8 - - + +
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Residues in contact with THR 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A SER* 2.9 8.2 + - - -
320A LEU* 1.3 82.1 - - + +
322A SER* 1.3 61.5 + - - +
324A ILE* 3.6 11.0 + - - +
325A GLU* 3.3 21.8 + - - +
18B ASP* 5.4 3.8 + - - -
21B ASN* 3.8 27.1 + - - +
22B TYR* 4.8 19.1 - - + -
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Residues in contact with SER 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A GLU* 3.4 37.5 - - - +
288A TRP* 3.9 2.6 - - - -
318A LYS* 3.9 13.5 - - - +
319A SER* 2.6 39.7 + - - -
321A THR* 1.3 80.4 + - - +
323A ILE* 1.3 58.2 + - - +
325A GLU* 3.5 3.9 + - - +
326A TYR* 3.0 28.4 + - - +
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Residues in contact with ILE 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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288A TRP* 3.9 15.7 - - + -
296A PHE* 3.7 27.3 - - + -
307A PHE* 4.1 20.2 - - + +
310A ILE* 4.7 6.5 - - + -
311A GLN* 3.4 39.3 - - + +
315A LEU* 4.0 8.3 - - + +
318A LYS* 3.9 22.7 - - + -
319A SER 3.7 12.3 - - - +
320A LEU* 2.9 11.5 + - + +
322A SER* 1.3 74.3 - - - +
324A ILE* 1.3 60.4 + - - +
326A TYR* 3.4 1.9 + - - +
327A TYR* 2.8 27.7 + - - +
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Residues in contact with ILE 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A PHE* 3.5 42.8 - - + -
320A LEU* 3.0 21.5 + - + +
321A THR* 3.7 7.2 - - - +
322A SER 3.2 0.2 - - - -
323A ILE* 1.3 76.1 - - - +
325A GLU* 1.3 58.9 + - - +
327A TYR* 2.9 28.4 + - + +
328A TYR* 3.2 32.2 + - + -
20B GLY 4.3 1.1 - - - +
21B ASN* 3.2 38.6 - - - +
22B TYR 5.1 0.9 - - - +
23B TYR* 3.8 24.7 - - + -
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Residues in contact with GLU 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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249A ILE* 5.5 2.3 - - - +
283A ASP* 4.0 4.7 - - - +
284A GLU* 3.4 31.6 + - + +
321A THR 3.3 10.7 + - - +
322A SER* 3.8 4.7 - - - +
324A ILE* 1.3 79.2 - - - +
326A TYR* 1.3 61.7 + - - +
328A TYR* 3.7 5.7 + - - +
329A MET* 3.3 47.2 + - + +
21B ASN* 3.2 28.5 + - - +
33B HIS* 6.5 0.2 - - - -
36B ARG* 3.3 27.0 + - - +
333B TYR* 4.9 1.5 + - - +
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Residues in contact with TYR 326 (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 GLU* 3.4 29.3 - - + +
285A MET* 3.8 27.7 - - + -
288A TRP* 3.4 47.1 - + + -
293A ALA* 3.4 27.4 + - + +
296A PHE* 3.5 33.0 - + - -
297A GLU* 5.2 0.3 + - - -
322A SER 3.0 18.6 + - - +
323A ILE 3.5 3.8 - - - +
325A GLU* 1.3 75.5 - - - +
327A TYR* 1.3 69.0 + - - +
329A MET* 3.0 7.2 + - - +
330A TRP* 2.8 44.9 + + + +
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Residues in contact with TYR 327 (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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296A PHE* 3.8 20.0 - + + -
300A LEU* 3.7 20.4 - - + -
305A LYS* 3.0 25.2 + - + +
307A PHE* 3.3 39.3 - + + -
323A ILE 2.8 17.5 + - - +
324A ILE* 2.9 10.5 + - - +
326A TYR* 1.3 72.6 - - - +
328A TYR* 1.3 81.7 + + - +
330A TRP* 2.8 30.0 + + - +
331A LYS* 2.9 37.6 + - + +
401A IHP 2.8 29.0 + - - -
23B TYR* 6.1 0.2 - + - -
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Residues in contact with TYR 328 (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 PHE* 6.1 0.2 - + - -
324A ILE* 3.2 36.4 + - + +
325A GLU* 4.3 4.9 - - - +
327A TYR* 1.3 100.9 - + - +
329A MET* 1.3 62.5 + - - +
331A LYS* 3.3 21.2 + - + +
332A THR* 4.0 1.2 - - - +
401A IHP 3.1 27.5 + - - -
20B GLY 4.7 1.1 - - - -
23B TYR* 4.2 14.0 - + - -
31B LYS* 3.8 15.1 - - - +
32B PRO* 6.0 0.5 - - - +
33B HIS* 3.3 56.1 - + + +
305B ILE* 4.9 3.4 - - + -
333B TYR* 4.1 3.5 - - + -
336B TYR* 2.7 38.2 + + - +
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Residues in contact with MET 329 (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 ARG* 3.5 29.9 + - - +
283A ASP* 3.8 20.0 - - + +
285A MET* 3.7 37.6 - - + +
325A GLU* 3.3 44.6 + - + +
326A TYR 3.0 8.3 + - - +
328A TYR* 1.3 76.3 - - - +
330A TRP* 1.3 59.2 + - - +
332A THR* 3.1 24.8 + - - -
36B ARG* 3.8 8.1 - - - +
332B ASP* 4.6 7.9 - - - +
333B TYR* 3.7 29.8 - - + +
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Residues in contact with TRP 330 (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* 4.4 7.2 - - + -
296A PHE* 4.1 13.2 - + - -
297A GLU* 3.7 39.3 + - + +
300A LEU* 3.5 40.4 - - + -
326A TYR* 2.8 44.3 + + + +
327A TYR* 3.3 20.4 - + - +
329A MET* 1.3 73.8 - - - +
331A LYS* 1.3 58.3 + - + +
332A THR 3.0 4.9 - - - -
333A THR* 2.5 56.7 + - + +
336A TYR* 3.3 42.3 - + + +
338A GLN* 5.5 0.2 - - - -
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Residues in contact with LYS 331 (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 LYS* 5.5 0.4 - - - +
327A TYR* 2.9 55.7 + - + +
328A TYR* 3.5 17.8 - - + +
329A MET 3.3 0.2 - - - -
330A TRP* 1.3 82.5 - - + +
332A THR* 1.3 56.4 + - - +
333A THR 3.3 1.1 - - - -
336A TYR* 3.1 37.0 - - + +
401A IHP 3.0 71.2 + - - -
336B TYR* 3.8 25.5 + - + +
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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