Contacts of the helix formed by residues 320 - 333 (chain A) in PDB entry 1UU1
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 LYS 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A PRO* 3.6 24.1 + - + +
31A PHE* 3.6 28.3 - - + -
32A PRO* 4.5 10.1 - - - +
257A PHE* 4.7 5.4 - - - -
319A GLY* 1.3 75.3 - - - -
321A ARG* 1.3 67.8 + - - +
322A GLU* 3.2 23.3 - - + +
323A GLU* 2.6 34.0 + - - +
324A ASN* 3.0 11.7 + - - -
48B ASP* 5.6 2.0 + - - -
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Residues in contact with ARG 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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257A PHE* 3.4 37.0 - - + -
261A GLU* 3.0 24.5 + - - +
264A ARG* 4.2 10.8 - - - +
319A GLY 3.8 0.4 + - - -
320A LYS* 1.3 72.5 - - - +
322A GLU* 1.3 67.4 + - - +
324A ASN* 3.3 2.8 + - - +
325A ASP* 2.9 42.9 + - - +
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Residues in contact with GLU 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 LYS* 3.5 21.7 - - + +
321A ARG* 1.3 92.4 + - - +
323A GLU* 1.3 67.7 + - + +
325A ASP* 2.8 21.2 + - - +
326A MET* 2.9 14.9 + - - +
329A ARG* 4.9 0.9 + - - -
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Residues in contact with GLU 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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22A THR* 4.5 28.9 - - + +
23A TYR 5.1 2.6 + - - +
24A LEU* 4.4 23.8 - - + +
30A PRO* 4.8 1.2 - - - +
319A GLY* 3.2 9.2 - - - -
320A LYS* 2.6 47.2 + - + +
322A GLU* 1.3 77.8 - - + +
324A ASN* 1.3 61.1 + - - +
326A MET* 2.9 29.4 - - - +
327A ILE* 3.0 13.1 + - - +
51B ARG* 5.7 4.7 + - - -
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Residues in contact with ASN 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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24A LEU* 4.9 1.6 - - - +
261A GLU* 2.8 40.6 + - + +
264A ARG* 4.5 3.4 - - - +
265A MET* 3.5 36.2 - - + +
316A ILE* 6.0 0.2 - - - +
317A THR 4.3 2.6 - - - +
318A ILE* 3.8 4.0 - - - +
319A GLY 2.7 42.5 + - - -
320A LYS 3.0 7.2 + - - -
321A ARG 3.5 5.2 - - - +
323A GLU* 1.3 78.8 - - - +
325A ASP* 1.3 63.4 + - - +
327A ILE* 3.1 4.8 + - - +
328A LEU* 3.0 22.8 + - - +
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Residues in contact with ASP 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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264A ARG* 2.5 41.0 + - - +
321A ARG* 2.9 25.4 + - - +
322A GLU* 2.8 13.6 + - - +
324A ASN* 1.3 75.9 - - - +
326A MET* 1.3 62.1 + - - +
328A LEU* 3.1 7.2 + - - +
329A ARG* 2.9 38.6 + - - +
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Residues in contact with MET 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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22A THR* 4.9 9.0 - - + +
24A LEU* 5.7 0.9 - - - -
303A LYS* 4.5 17.9 - - + +
305A VAL* 3.4 35.2 - - + -
322A GLU 2.9 8.7 + - - +
323A GLU* 2.9 28.3 - - - +
325A ASP* 1.3 77.5 - - - +
327A ILE* 1.3 67.7 + - - +
329A ARG* 3.3 30.6 - - - +
330A GLU* 2.7 54.3 + - + +
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Residues in contact with ILE 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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24A LEU* 3.7 26.5 - - + -
265A MET* 3.4 22.9 - - + -
269A LEU* 5.7 0.7 - - + -
300A LEU* 5.2 7.6 - - + -
305A VAL* 4.3 7.6 - - + -
307A VAL* 4.3 12.8 - - + -
316A ILE* 4.1 22.7 - - + -
323A GLU 3.0 18.7 + - - +
324A ASN* 3.3 8.5 - - - +
326A MET* 1.3 86.9 - - - +
328A LEU* 1.3 67.6 + - + +
330A GLU* 3.4 4.0 + - + +
331A LEU* 3.0 42.3 + - + +
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Residues in contact with LEU 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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264A ARG* 4.2 25.8 - - + +
265A MET* 4.1 31.4 - - + +
268A ALA* 3.8 30.3 - - + -
269A LEU* 3.6 31.9 - - + -
272A MET* 3.9 8.0 - - - +
324A ASN 3.0 16.2 + - - +
325A ASP* 3.6 6.3 - - - +
327A ILE* 1.3 76.7 - - + +
329A ARG* 1.3 58.2 + - + +
331A LEU* 3.4 4.0 + - - +
332A GLU* 2.8 29.8 + - - +
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Residues in contact with ARG 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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303A LYS* 5.3 8.9 - - - +
322A GLU 4.9 0.6 + - - -
325A ASP* 2.9 23.7 + - - +
326A MET* 3.3 44.0 + - - +
328A LEU* 1.3 75.7 - - - +
330A GLU* 1.3 69.6 + - + +
332A GLU* 3.0 17.8 + - - +
333A VAL* 2.9 30.4 + - + +
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Residues in contact with GLU 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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296A LEU* 5.3 4.3 - - + -
299A HIS* 2.7 38.2 + - + -
300A LEU* 4.3 18.8 - - + -
303A LYS* 3.3 30.5 - - - +
326A MET* 2.7 43.2 + - + +
327A ILE* 3.7 7.4 - - + +
329A ARG* 1.3 77.6 + - + +
331A LEU* 1.3 63.9 + - + +
332A GLU 3.1 1.0 + - - -
333A VAL* 3.1 24.8 - - - +
334A PHE* 3.3 11.7 + - - +
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Residues in contact with LEU 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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269A LEU* 3.5 27.1 - - + -
272A MET* 3.1 9.5 - - + +
274A TYR* 2.7 48.6 + - + +
286A VAL* 4.6 8.7 - - + -
288A MET* 4.9 2.0 - - + -
296A LEU* 3.5 34.8 - - + -
314A VAL* 5.9 0.4 - - + -
316A ILE* 4.1 17.7 - - + -
327A ILE* 3.0 36.2 + - + +
328A LEU 3.9 4.0 - - - +
330A GLU* 1.3 77.7 - - + +
332A GLU* 1.3 60.5 + - - +
334A PHE* 3.1 10.6 + - + +
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Residues in contact with GLU 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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272A MET* 3.0 23.8 - - + +
328A LEU 2.8 14.9 + - - +
329A ARG* 3.0 21.4 + - - +
331A LEU* 1.3 73.6 - - - +
333A VAL* 1.3 59.9 + - + +
334A PHE 2.7 25.2 + - - +
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Residues in contact with VAL 333 (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 HIS* 5.0 4.3 - - - +
329A ARG* 2.9 19.1 + - + +
330A GLU* 3.1 31.0 - - - +
332A GLU* 1.3 79.3 - - + +
334A PHE* 1.3 59.5 + - + +
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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