Contacts of the strand formed by residues 313 - 317 (chain D) 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 GLY 313 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285D PHE* 3.8 9.1 - - - -
286D VAL 3.2 11.4 - - - -
288D MET 3.7 6.7 - - - -
293D LYS* 3.4 17.1 - - - +
310D PHE 2.9 29.6 + - - +
311D ARG 3.6 0.2 - - - -
312D GLU* 1.3 80.8 - - - +
314D VAL* 1.3 65.9 + - - +
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Residues in contact with VAL 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284D VAL 3.9 0.7 - - - +
285D PHE* 3.4 8.2 - - - -
286D VAL* 2.9 56.0 + - + +
288D MET* 4.5 8.1 - - - -
293D LYS* 4.0 9.9 - - + -
296D LEU* 4.5 11.4 - - + -
297D LEU* 3.8 29.4 - - + -
307D VAL* 4.5 10.5 - - + -
308D ARG 3.4 9.0 - - - +
309D SER* 4.8 2.5 - - - -
313D GLY* 1.3 78.9 - - - +
315D ARG* 1.3 62.0 + - - +
316D ILE* 4.0 14.3 + - + -
331D LEU* 6.2 1.6 - - + -
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Residues in contact with ARG 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D LEU 3.9 2.1 - - - +
25D ALA 3.8 13.5 + - - -
26D LEU* 4.0 2.2 - - - +
27D ASN* 3.3 39.9 + - - +
149D ASN* 3.5 21.2 + - - +
150D PRO* 3.5 17.3 - - - +
283D PHE* 3.4 27.3 - - + -
284D VAL 3.5 2.7 - - - +
285D PHE* 3.8 10.1 - - + -
308D ARG* 2.8 58.6 + - - +
310D PHE* 3.8 19.1 - - + -
314D VAL* 1.3 74.3 - - - +
316D ILE* 1.3 59.3 + - - +
317D THR* 3.9 2.5 + - - -
1336D HSA 3.0 38.8 + - - -
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Residues in contact with ILE 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D LEU* 4.1 12.8 - - + -
265D MET* 5.4 5.4 - - - -
269D LEU* 5.6 0.4 - - + -
283D PHE* 3.0 3.4 - - - +
284D VAL* 2.9 44.6 + - + +
286D VAL* 4.3 8.1 - - + -
296D LEU* 6.0 0.2 - - + -
300D LEU* 5.4 4.0 - - + -
307D VAL* 3.5 23.8 - - + -
314D VAL* 4.3 20.6 - - + +
315D ARG* 1.3 74.2 - - - +
317D THR* 1.3 65.1 + - - +
318D ILE* 3.8 0.9 + - - +
327D ILE* 3.8 40.2 - - + -
331D LEU* 4.1 27.8 - - + -
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Residues in contact with THR 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D TYR 5.8 0.2 - - - +
24D LEU* 2.9 55.5 + - + +
25D ALA* 4.3 0.3 - - - -
26D LEU 3.7 1.4 + - - -
27D ASN* 2.7 49.5 + - - -
28D GLU 3.7 14.8 - - - +
265D MET* 5.9 0.6 - - - +
282D ASN* 3.7 7.0 - - - +
283D PHE* 3.6 5.8 - - - -
315D ARG* 3.9 1.1 + - - -
316D ILE* 1.3 75.6 - - - +
318D ILE* 1.3 77.9 + - - +
319D GLY 3.3 0.5 + - - -
324D ASN* 4.7 0.5 - - - +
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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