Contacts of the strand formed by residues 283 - 287 (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 PHE 283 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D ASN* 3.3 42.2 - - - +
148D ASN 3.8 7.0 - - - -
149D ASN* 4.8 2.5 - - - -
150D PRO* 2.9 30.5 - - + -
151D THR 4.0 1.6 - - - -
152D GLY* 3.7 25.8 - - - -
176D TYR* 3.8 20.4 - + - -
262D ARG* 3.7 5.0 - - - -
279D SER* 2.4 35.9 + - - -
281D GLY* 3.3 3.7 + - - -
282D ASN* 1.3 90.8 - - - +
284D VAL* 1.3 69.2 + - - +
315D ARG* 3.4 15.7 - - + -
316D ILE 3.0 18.2 - - - +
317D THR* 3.6 1.6 - - - -
318D ILE* 3.4 10.7 - - - +
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Residues in contact with VAL 284 (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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262D ARG* 3.9 13.5 - - + +
265D MET* 4.4 13.5 - - + -
266D LYS* 3.5 33.0 - - + +
269D LEU* 4.1 22.4 - - + -
276D ILE* 5.9 2.0 - - + -
277D THR 5.9 0.4 - - - +
279D SER* 4.1 4.0 - - - -
283D PHE* 1.3 85.0 - - - +
285D PHE* 1.3 62.3 + - - +
286D VAL* 4.8 5.2 - - + -
314D VAL 3.9 0.2 - - - +
315D ARG* 3.5 5.2 - - - +
316D ILE* 2.9 51.6 + - + +
318D ILE* 4.2 7.6 - - + -
327D ILE* 6.1 0.7 - - + -
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Residues in contact with PHE 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D PRO* 6.1 0.2 - - + -
150D PRO* 3.1 48.7 - - + +
151D THR* 4.0 9.2 - - + +
276D ILE* 3.2 9.2 - - - +
277D THR* 3.1 60.7 + - + +
279D SER* 4.6 1.0 - - - -
283D PHE* 4.6 0.2 - - - -
284D VAL* 1.3 75.7 - - - +
286D VAL* 1.3 73.7 + - - +
287D PHE* 3.8 26.5 - + - -
310D PHE* 3.9 17.7 - + + -
312D GLU* 4.2 7.9 - - + -
313D GLY* 3.8 24.9 - - - -
314D VAL 3.4 12.1 - - - -
315D ARG* 3.8 5.2 - - + -
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Residues in contact with VAL 286 (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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269D LEU* 4.1 25.4 - - + -
274D TYR* 3.8 32.8 - - + -
275D ARG 3.7 7.9 - - - +
276D ILE* 4.5 2.2 - - + +
284D VAL* 4.8 2.9 - - + -
285D PHE* 1.3 80.5 - - - +
287D PHE* 1.3 66.2 + - - +
288D MET* 3.7 17.6 - - + +
313D GLY* 3.2 2.1 - - - -
314D VAL* 2.9 49.8 + - + +
316D ILE* 4.3 13.9 - - + -
331D LEU* 4.7 5.8 - - + -
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Residues in contact with PHE 287 (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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127D LYS* 4.7 13.5 - - - -
129D LEU* 4.2 23.8 - - + -
151D THR* 4.9 4.3 - - + -
274D TYR* 5.4 1.0 - - - -
275D ARG* 2.7 86.8 + - + +
276D ILE 4.4 5.4 - - - -
277D THR* 3.3 31.0 - - + -
285D PHE* 3.8 16.2 - + - -
286D VAL* 1.3 73.2 - - - +
288D MET* 1.3 68.7 + - - +
292D GLU* 5.2 0.5 - - - +
312D GLU* 3.4 27.1 - - + +
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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