Contacts of the strand formed by residues 155 - 158 (chain H) in PDB entry 2POZ
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 ALA 155 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125H ARG* 5.3 1.3 - - - +
126H ALA 4.7 2.1 + - - +
127H TYR* 3.4 24.0 - - + -
128H ALA 3.0 21.5 + - - -
153H TYR* 3.4 4.1 - - - +
154H GLY* 1.3 81.5 - - - +
156H LEU* 1.3 70.1 + - - +
200H ILE* 4.3 0.6 - - - +
201H GLU* 3.2 30.3 - - + +
203H MSE 3.9 9.6 - - + -
330H ILE* 4.1 6.3 - - + -
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Residues in contact with LEU 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127H TYR* 5.0 0.7 - - - -
128H ALA* 3.6 13.2 - - + +
131H TRP* 3.6 33.9 - - + +
145H VAL* 4.2 19.3 - - + -
148H PRO* 3.9 26.9 - - + -
149H LEU* 4.1 21.8 - - + -
153H TYR* 4.4 3.1 - - + -
155H ALA* 1.3 84.7 - - - +
157H LYS* 1.3 55.3 + - - +
158H PHE* 4.5 1.3 - - - -
192H VAL* 4.6 0.4 - - + -
196H ALA* 4.7 2.0 - - + -
200H ILE* 4.1 10.1 - - + -
201H GLU 2.8 9.3 + - - +
202H LEU* 3.4 22.2 - - + +
203H MSE 2.8 35.1 + - - +
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Residues in contact with LYS 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127H TYR* 2.9 43.8 + - + +
128H ALA 3.0 9.4 + - - +
129H ASN* 3.1 30.3 - - - +
131H TRP* 2.8 20.8 + - - -
132H TYR* 3.7 6.2 - - - -
156H LEU* 1.3 74.8 - - - +
158H PHE* 1.3 69.6 + - - +
203H MSE 3.2 27.4 - - + +
205H ASP* 3.8 18.3 + - + +
229H PHE* 4.8 3.4 - - + -
231H GLU* 2.8 35.8 + - + +
278H GLN* 4.3 1.2 - - - +
307H HIS* 4.9 4.2 - - - -
332H GLU* 3.2 10.9 + - - -
334H TYR* 5.2 0.2 + - - -
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Residues in contact with PHE 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H ASN* 5.1 0.9 - - - -
131H TRP* 3.8 16.8 - + + -
132H TYR* 3.6 24.2 - - + -
141H PHE* 3.9 21.5 - + + -
156H LEU 4.5 1.1 - - - -
157H LYS* 1.3 81.2 - - - +
159H TYR* 1.3 58.9 + - - +
160H PRO* 3.3 18.6 - - + +
188H ARG* 4.4 1.3 - - + -
189H VAL* 3.9 42.0 - - + -
192H VAL* 3.9 35.2 - - + -
202H LEU* 4.5 14.6 - - + -
203H MSE 3.1 14.1 + - - -
204H VAL* 3.6 12.3 - - + -
205H ASP* 3.0 25.2 + - - -
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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