Contacts of the helix formed by residues 320 - 332 (chain A) in PDB entry 1UEC
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 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A ARG 3.6 2.1 + - - -
319A LEU* 1.3 77.0 - - - +
321A GLN* 1.3 63.7 + - - +
322A ASP* 3.4 10.5 + - - +
323A ALA* 3.1 24.1 + - - +
324A TYR* 3.0 21.4 + - - -
326A ARG* 5.2 1.2 + - - -
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Residues in contact with GLN 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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243A ASP* 3.8 28.5 - - + -
265A VAL* 3.9 7.4 - - - +
272A THR* 2.9 54.3 + - - +
273A GLY* 3.2 10.7 + - - -
274A TYR* 3.2 34.5 + - + -
319A LEU 4.7 0.2 + - - -
320A SER* 1.3 75.2 - - - +
322A ASP* 1.3 58.1 + - - +
324A TYR* 3.5 19.9 - - - +
325A ARG* 2.8 27.6 + - - +
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Residues in contact with ASP 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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320A SER* 3.1 9.9 + - - +
321A GLN* 1.3 79.2 - - - +
323A ALA* 1.3 56.7 + - - +
325A ARG* 3.2 31.1 + - - +
326A ARG* 2.9 59.4 + - - +
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Residues in contact with ALA 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 LEU* 4.0 19.5 - - + -
320A SER* 3.1 25.8 + - - +
322A ASP* 1.3 77.2 + - - +
324A TYR* 1.3 64.6 + - - +
326A ARG* 3.3 24.4 + - - +
327A ASN* 3.1 31.4 + - - +
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Residues in contact with TYR 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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224A PRO* 4.7 2.0 - - + -
226A TYR* 3.9 20.7 - + - -
256A ILE* 3.8 24.9 - - + -
257A HIS* 2.7 38.6 + + + -
259A LEU* 4.3 0.5 - - - +
265A VAL* 3.7 19.1 - - + +
272A THR* 3.6 15.0 - - + +
274A TYR* 4.2 5.6 - - - -
318A ARG* 3.8 15.2 - - - -
319A LEU* 3.4 37.4 + - + +
320A SER 3.0 20.9 + - - -
321A GLN* 3.5 26.0 - - - +
323A ALA* 1.3 76.2 - - - +
325A ARG* 1.3 57.3 + - - +
327A ASN* 3.3 4.2 + - - +
328A SER* 2.8 30.6 + - - -
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Residues in contact with ARG 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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270A ASP 3.8 23.5 + - - +
271A VAL* 4.4 19.5 - - - +
272A THR* 3.5 10.0 + - + +
321A GLN 2.8 18.3 + - - +
322A ASP* 3.4 27.3 + - - +
323A ALA 3.2 0.2 - - - -
324A TYR* 1.3 75.1 - - - +
326A ARG* 1.3 74.5 + - - +
328A SER* 3.1 5.9 + - - -
329A VAL* 2.9 48.4 + - + +
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Residues in contact with ARG 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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320A SER* 5.2 1.2 + - - -
322A ASP* 2.9 39.4 + - - +
323A ALA* 3.3 24.9 + - - +
325A ARG* 1.3 92.9 - - - +
327A ASN* 1.3 65.5 + - - +
329A VAL* 3.3 10.1 - - - +
330A ARG* 3.1 42.7 + - - +
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Residues in contact with ASN 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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226A TYR* 3.0 45.2 + - + -
319A LEU* 3.9 13.5 - - - +
323A ALA* 3.1 17.9 + - - +
324A TYR 3.7 1.8 - - - +
326A ARG* 1.3 77.5 - - - +
328A SER* 1.3 62.0 + - - +
330A ARG 3.2 0.9 + - - -
331A PHE* 2.9 50.4 + - + +
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Residues in contact with SER 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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226A TYR* 3.8 16.4 - - - -
256A ILE* 5.1 3.7 - - - +
267A ARG* 2.9 36.3 + - - +
270A ASP 5.5 1.0 + - - -
272A THR* 3.8 18.6 - - - +
324A TYR 2.8 18.0 + - - -
325A ARG* 3.4 4.9 - - - -
327A ASN* 1.3 78.6 - - - +
329A VAL* 1.3 64.6 + - - +
330A ARG 3.2 0.7 + - - -
332A LEU* 3.1 30.0 + - - +
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Residues in contact with VAL 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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267A ARG* 6.0 1.1 - - - +
270A ASP* 3.9 28.0 - - + +
325A ARG* 2.9 36.4 + - + +
326A ARG* 3.3 18.6 - - - +
328A SER* 1.3 74.9 - - - +
330A ARG* 1.3 75.8 + - + +
332A LEU* 3.3 19.0 - - - +
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Residues in contact with ARG 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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326A ARG* 3.1 40.0 + - - +
327A ASN 3.2 1.0 + - - -
328A SER 3.1 0.8 - - - -
329A VAL* 1.3 93.6 - - + +
331A PHE* 1.3 90.6 + - + +
332A LEU* 3.6 4.9 + - - +
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Residues in contact with PHE 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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226A TYR* 3.5 32.5 - + + +
227A ALA* 3.6 4.2 + - - +
327A ASN* 2.9 42.5 + - + +
330A ARG* 1.3 103.7 - - + +
332A LEU* 1.3 65.2 + - - +
333A GLN* 4.0 5.5 - - - +
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Residues in contact with LEU 332 (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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226A TYR 3.1 10.5 - - - +
267A ARG* 3.7 29.8 - - - +
328A SER 3.1 14.1 + - - +
329A VAL* 3.3 26.2 - - - +
330A ARG 4.3 5.0 - - - +
331A PHE* 1.3 81.1 - - - +
333A GLN* 1.3 77.1 + - - +
334A GLN* 3.8 25.8 - - + +
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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