Contacts of the helix formed by residues 320 - 333 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30C PRO* 3.7 21.3 - - + +
31C PHE* 4.2 22.9 - - + -
257C PHE* 4.6 4.7 - - - -
319C GLY* 1.3 73.2 - - - -
321C ARG* 1.3 60.6 - - - +
322C GLU* 3.2 28.8 + - - +
323C GLU* 2.8 28.3 + - + +
324C ASN* 2.9 28.7 + - - -
48D ASP* 6.1 0.9 - - - -
51D ARG* 6.2 1.6 - - - +
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Residues in contact with ARG 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C PHE* 3.7 33.8 - - + -
261C GLU* 3.7 20.0 - - - +
264C ARG* 5.6 1.6 - - - +
320C LYS* 1.3 73.2 - - - +
322C GLU* 1.3 69.3 + - - +
324C ASN* 3.3 2.8 + - - +
325C ASP* 3.0 38.9 + - - +
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Residues in contact with GLU 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320C LYS* 3.2 36.3 + - - +
321C ARG* 1.3 81.5 + - - +
323C GLU* 1.3 64.9 + - + +
325C ASP* 3.2 9.5 + - - +
326C MET* 2.8 30.4 + - - +
329C ARG* 4.5 1.2 + - - -
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Residues in contact with GLU 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C LYS 5.1 0.5 - - - +
22C THR* 3.3 33.0 + - - +
23C TYR 5.0 1.0 + - - +
24C LEU* 4.3 14.5 - - + +
30C PRO* 4.8 1.9 - - - +
319C GLY* 3.5 11.5 - - - -
320C LYS* 2.8 51.7 + - + +
322C GLU* 1.3 85.4 - - + +
324C ASN* 1.3 63.6 + - - +
326C MET* 3.2 11.3 + - - +
327C ILE* 3.1 26.5 + - - +
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Residues in contact with ASN 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C LEU* 5.6 1.7 - - - +
257C PHE* 4.5 0.2 - - - -
261C GLU* 2.7 46.5 + - + +
264C ARG* 4.4 2.2 - - - +
265C MET* 3.7 28.9 - - + +
317C THR 4.7 0.5 - - - +
318C ILE* 3.8 3.0 - - - +
319C GLY 2.9 43.0 + - - -
320C LYS 2.9 14.4 + - - -
321C ARG 3.3 0.6 + - - +
323C GLU* 1.3 75.7 - - - +
325C ASP* 1.3 62.6 + - - +
327C ILE* 3.4 8.0 + - - +
328C LEU* 3.3 28.4 + - - +
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Residues in contact with ASP 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C ARG* 3.2 34.1 + - - +
321C ARG* 3.0 25.8 + - - +
322C GLU* 3.4 12.2 - - - +
323C GLU 3.1 0.2 - - - -
324C ASN* 1.3 74.7 - - - +
326C MET* 1.3 65.2 + - - +
328C LEU* 3.5 7.9 + - - +
329C ARG* 3.1 38.9 + - + +
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Residues in contact with MET 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C THR* 4.0 15.3 - - + +
24C LEU* 4.6 1.8 - - + -
300C LEU* 5.0 0.4 - - - -
303C LYS* 5.4 4.5 - - + -
305C VAL* 3.5 33.4 - - + -
322C GLU 2.8 13.2 + - - +
323C GLU* 3.4 12.1 - - - +
325C ASP* 1.3 76.2 - - - +
327C ILE* 1.3 89.3 + - + +
329C ARG* 3.1 29.1 + - - +
330C GLU* 2.8 53.3 + - + +
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Residues in contact with ILE 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C LEU* 3.8 23.8 - - + -
265C MET* 3.8 22.7 - - + -
300C LEU* 4.8 8.7 - - + -
305C VAL* 4.0 11.0 - - + -
307C VAL* 4.7 3.8 - - + -
316C ILE* 4.2 18.6 - - + -
323C GLU 3.1 18.1 + - - +
324C ASN* 3.5 9.9 - - - +
325C ASP 3.3 0.2 - - - -
326C MET* 1.3 98.9 - - + +
328C LEU* 1.3 54.5 + - + +
330C GLU* 2.9 5.2 + - - +
331C LEU* 2.6 57.4 + - + +
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Residues in contact with LEU 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264C ARG* 4.2 24.0 - - - +
265C MET* 4.0 29.2 - - + +
268C ALA* 3.7 26.7 - - + -
269C LEU* 3.6 34.5 - - + -
272C MET* 3.4 13.0 - - + +
324C ASN 3.3 15.5 + - - +
325C ASP* 3.9 5.4 - - - +
326C MET 3.4 0.2 - - - -
327C ILE* 1.3 76.3 - - + +
329C ARG* 1.3 53.7 + - + +
331C LEU* 3.5 2.2 - - - +
332C GLU* 2.7 37.6 + - - +
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Residues in contact with ARG 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322C GLU 4.5 1.2 + - - -
325C ASP* 3.1 29.6 + - + +
326C MET* 3.2 53.0 - - - +
328C LEU* 1.3 76.0 - - + +
330C GLU* 1.3 71.7 + - - +
332C GLU* 3.3 14.0 + - - +
333C VAL* 2.9 24.3 + - - +
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Residues in contact with GLU 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296C LEU* 5.6 0.7 - - + +
299C HIS* 2.9 31.7 + - + +
300C LEU* 4.5 13.5 - - + -
303C LYS* 3.0 31.0 - - + +
326C MET* 2.8 38.0 + - - +
327C ILE* 3.4 7.4 - - - +
329C ARG* 1.3 94.2 + - - +
331C LEU* 1.3 68.4 + - + +
333C VAL* 3.1 22.7 + - - +
334C PHE* 3.6 11.1 + - - +
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Residues in contact with LEU 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269C LEU* 3.3 29.2 - - + -
272C MET* 3.8 2.0 - - - -
274C TYR* 2.3 49.4 + - + +
286C VAL* 4.7 8.1 - - + -
296C LEU* 4.2 31.0 - - + -
300C LEU* 5.2 5.6 - - + -
314C VAL* 6.3 0.4 - - + -
316C ILE* 4.2 17.5 - - + -
327C ILE* 2.6 40.8 + - + +
328C LEU 3.9 2.9 - - - +
330C GLU* 1.3 79.8 - - + +
332C GLU* 1.3 60.8 + - - +
333C VAL 3.3 0.7 + - - -
334C PHE* 3.4 4.1 + - + -
335C LYS 3.0 9.0 - - - +
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Residues in contact with GLU 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C MET* 3.4 29.5 - - + +
328C LEU 2.7 22.4 + - - +
329C ARG* 3.7 10.5 - - - +
330C GLU 3.2 0.6 - - - -
331C LEU* 1.3 74.2 - - - +
333C VAL* 1.3 64.2 + - + +
335C LYS 3.2 11.7 - - - +
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Residues in contact with VAL 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299C HIS* 5.4 4.5 - - + -
329C ARG 2.9 21.8 - - - +
330C GLU* 3.1 23.3 - - - +
332C GLU* 1.3 86.0 - - + +
334C PHE* 1.3 60.7 + - - +
335C LYS 4.5 0.4 - - - -
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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