Contacts of the strand formed by residues 204 - 208 (chain X) in PDB entry 1UL1
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 ILE 204 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20X GLU* 3.7 0.7 - - - -
21X ASN* 3.0 35.8 + - - +
23X ILE* 3.4 42.1 - - + +
26X TYR* 3.9 20.5 + - + +
191X MET* 3.6 33.2 - - + -
192X ARG 3.3 13.5 - - - +
193X HIS* 4.0 11.7 - - - +
194X LEU* 3.2 33.2 - - + -
202X LEU 3.8 2.1 + - - +
203X PRO* 1.3 71.3 - - - +
205X GLN* 1.3 60.7 + - - +
206X GLU 4.1 0.5 + - - -
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Residues in contact with GLN 205 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18X ILE* 4.2 15.8 - - + +
19X ARG 3.5 7.6 - - - +
20X GLU* 4.3 16.0 + - + +
190X LEU 3.6 1.9 - - - +
191X MET* 3.1 3.8 - - - -
192X ARG* 2.6 88.3 + - + +
193X HIS* 3.7 17.8 - - - +
203X PRO 3.2 4.0 + - - +
204X ILE* 1.3 71.8 - - - +
206X GLU* 1.3 59.9 + - - +
207X PHE* 3.6 24.6 - - + -
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Residues in contact with GLU 206 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17X ALA 3.2 12.3 - - - +
18X ILE* 4.6 0.2 - - - -
19X ARG* 2.8 68.3 + - + +
21X ASN* 3.8 6.2 + - - +
26X TYR* 3.3 28.6 - - - +
173X TYR* 2.7 39.3 + - - -
189X VAL* 3.9 17.3 - - + -
190X LEU 3.5 4.3 - - - +
191X MET* 4.1 6.2 - - + +
204X ILE 4.1 0.6 + - - -
205X GLN* 1.3 70.9 - - - +
207X PHE* 1.3 62.8 + - - +
208X HIS* 3.7 8.9 + - - +
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Residues in contact with PHE 207 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7X ALA* 4.6 4.9 - - + -
10X ILE* 4.0 21.1 - - + -
17X ALA 3.3 5.2 - - - -
18X ILE* 3.3 37.5 - - + -
180X MET* 3.5 32.1 - - + -
183X LEU* 4.0 17.7 - - + +
189X VAL* 3.6 7.8 - - - +
190X LEU* 2.8 42.9 + - + +
192X ARG* 3.5 24.5 - - + -
205X GLN* 3.6 37.0 - - + -
206X GLU* 1.3 75.2 - - - +
208X HIS* 1.3 61.1 + - - +
209X LEU 3.9 0.9 + - - -
212X ILE* 4.7 3.4 - - + -
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Residues in contact with HIS 208 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A GLU* 3.6 27.8 + - + -
16X SER 5.8 0.9 - - - -
17X ALA* 3.0 16.9 + - - +
19X ARG* 3.2 31.2 + - + -
173X TYR* 4.0 10.5 - + - -
188X PRO 3.8 2.7 + - - -
189X VAL* 3.8 29.7 - - + +
206X GLU* 3.4 15.2 + - + -
207X PHE* 1.3 75.6 - - - +
209X LEU* 1.3 67.6 + - - +
210X SER* 3.3 3.5 + - - +
211X ARG* 3.2 44.7 + - + +
212X ILE* 3.2 14.0 + - - +
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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