Contacts of the strand formed by residues 305 - 310 (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 VAL 305 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20C ASP* 4.6 1.8 - - - +
22C THR* 3.2 22.4 - - + +
24C LEU* 4.6 3.4 - - + -
300C LEU* 2.8 43.7 + - + +
301C ARG* 3.9 8.1 + - - +
303C LYS* 3.7 20.0 - - + +
304C ASN* 1.3 77.6 - - - +
306C ALA* 1.3 64.1 + - - +
307C VAL* 4.3 11.2 - - + +
326C MET* 3.5 36.8 - - + -
327C ILE* 4.0 14.8 - - + -
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Residues in contact with ALA 306 (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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18C LYS 5.8 0.9 - - - +
20C ASP* 4.0 15.7 - - + +
22C THR 2.8 8.0 + - - +
23C TYR* 3.6 31.0 - - + -
24C LEU* 2.7 33.8 + - - +
25C ALA* 4.2 2.2 - - + -
305C VAL* 1.3 73.9 - - - +
307C VAL* 1.3 65.1 + - - +
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Residues in contact with VAL 307 (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* 3.9 7.4 - - + +
25C ALA* 3.4 10.5 - - - +
297C LEU* 3.9 22.3 - - + +
300C LEU* 3.7 32.5 - - + -
305C VAL* 4.4 8.7 - - + -
306C ALA* 1.3 81.5 - - - +
308C ARG* 1.3 64.0 + - - +
309C SER* 3.6 2.9 + - - -
314C VAL* 4.5 10.3 - - + -
315C ARG 3.9 7.2 - - - +
316C ILE* 3.9 34.5 - - + -
327C ILE* 4.7 1.6 - - + -
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Residues in contact with ARG 308 (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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17C GLU* 3.1 39.5 + - - -
23C TYR* 4.6 6.2 + - - -
25C ALA* 3.3 30.7 + - - +
26C LEU* 4.0 11.3 - - - +
307C VAL* 1.3 72.2 + - - +
309C SER* 1.3 66.7 + - - +
310C PHE* 3.2 30.0 - - + -
314C VAL* 3.4 5.6 - - - +
315C ARG* 2.8 52.8 + - - +
1336C HSA 3.3 21.7 + - - -
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Residues in contact with SER 309 (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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293C LYS* 3.8 17.5 + - - +
297C LEU* 3.7 31.5 - - - +
307C VAL 3.6 3.7 + - - -
308C ARG* 1.3 82.2 + - - +
310C PHE* 1.3 68.6 + - - +
313C GLY 4.1 2.2 - - - -
314C VAL* 4.6 3.4 - - - -
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Residues in contact with PHE 310 (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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104C PRO* 5.9 3.4 - - + -
105C THR 5.0 6.5 - - - -
107C SER* 5.1 9.6 - - - -
149C ASN* 4.8 0.4 - - - -
150C PRO* 3.4 41.3 - - + -
285C PHE* 3.7 26.7 - + + -
293C LYS* 2.6 27.2 + - - -
308C ARG* 3.2 32.5 - - + -
309C SER* 1.3 77.6 + - - +
311C ARG* 1.3 59.9 + - - +
312C GLU 4.3 1.6 - - - +
313C GLY 2.9 21.4 + - - +
315C ARG* 3.5 22.4 - - + -
1336C HSA 4.0 8.7 - - - -
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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