Contacts of the strand formed by residues 219 - 223 (chain A) in PDB entry 1P0P
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 ARG 219 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A SER* 4.8 4.9 + - - -
192A VAL 3.3 2.8 + - - -
193A THR* 3.7 12.7 + - - +
194A LEU 3.0 23.7 + - - -
217A PHE* 3.2 12.9 - - - -
218A THR* 1.3 98.7 - - - +
220A ALA* 1.3 62.4 + - - +
315A THR* 3.6 10.3 - - - +
316A GLN* 2.7 43.7 + - - +
474A PHE* 2.9 41.5 + - + -
475A ALA 3.2 20.2 + - - -
476A LYS 3.6 15.2 + - - -
477A TYR 4.2 2.0 + - - -
478A GLY* 3.5 19.7 - - - +
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Residues in contact with ALA 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LEU* 3.3 6.1 - - + +
204A VAL* 3.4 24.7 - - + -
208A LEU* 4.1 25.1 - - + -
217A PHE* 4.2 3.6 - - + -
219A ARG* 1.3 79.8 - - - +
221A ILE* 1.3 63.9 + - - +
222A LEU* 3.8 7.6 - - + -
316A GLN 3.6 4.8 + - - -
317A ILE* 3.3 9.4 - - + +
318A LEU 3.0 22.5 + - - +
474A PHE* 3.5 3.8 - - - -
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Residues in contact with ILE 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LEU* 5.0 4.0 - - + -
193A THR* 4.0 15.9 - - + -
194A LEU 2.8 7.7 + - - +
195A PHE* 3.3 36.4 - - + -
196A GLY 3.4 6.4 + - - -
204A VAL* 4.1 4.7 - - - +
220A ALA* 1.3 76.5 - - - +
222A LEU* 1.3 66.5 + - - +
223A GLN* 4.0 13.7 - - + +
318A LEU* 3.2 22.4 - - + +
471A TRP* 3.7 50.3 - - + +
474A PHE* 3.7 28.9 - - + -
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Residues in contact with LEU 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A ALA* 3.9 11.0 - - + +
204A VAL* 3.7 21.1 - - + -
205A SER* 3.5 32.3 - - - -
208A LEU* 4.7 2.5 - - + -
220A ALA* 3.8 11.2 - - + +
221A ILE* 1.3 85.1 - - - +
223A GLN* 1.3 63.0 + - - +
224A SER 3.8 0.2 + - - -
225A GLY 3.6 20.4 + - - +
226A SER* 4.6 1.8 - - - -
317A ILE* 4.7 5.2 - - + -
318A LEU 2.7 14.6 + - - +
319A VAL* 3.4 17.0 - - + +
320A GLY 3.2 24.1 + - - +
405A PHE* 3.9 23.6 - - + -
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Residues in contact with GLN 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A TRP* 4.4 7.9 - - - -
195A PHE* 4.0 8.0 - - - -
196A GLY 3.1 16.2 + - - +
197A GLU* 3.2 10.8 - - + +
198A SER 2.9 20.6 + - - -
201A ALA* 3.6 1.1 - - - +
221A ILE* 4.0 14.6 - - + +
222A LEU* 1.3 71.7 - - - +
224A SER* 1.3 70.4 + - - +
225A GLY 3.4 0.6 + - - -
419A TYR* 3.1 24.9 - - + +
441A GLU* 2.9 32.0 + - - +
442A ILE* 4.3 6.3 - - - +
445A VAL* 3.7 19.4 - - - +
471A TRP* 3.0 26.2 + - - +
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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