Contacts of the strand formed by residues 219 - 223 (chain A) in PDB entry 2IHU
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 PRO 219 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A LEU* 3.6 32.8 - - + -
216A ALA* 4.2 3.1 - - + -
217A LYS 3.6 7.9 - - - +
218A HIS* 1.3 90.3 - - - +
220A VAL* 1.3 62.6 + - - +
245A ILE* 3.5 11.8 - - + +
246A PRO* 3.3 24.5 - - + +
289A ASP* 3.9 0.2 - - - -
290A LEU* 3.4 24.2 - - + +
292A LEU* 4.6 3.4 - - + -
356A LYS* 3.8 28.3 - - + -
357A GLN 5.2 1.1 - - - +
358A ARG* 6.0 1.3 - - - -
359A HIS* 5.1 0.7 + - - -
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Residues in contact with VAL 220 (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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219A PRO* 1.3 80.1 - - - +
221A LEU* 1.3 60.0 + - - +
222A VAL* 4.3 11.9 - - + -
245A ILE* 3.8 5.2 - - - -
246A PRO* 3.7 14.1 - - + +
248A ILE* 3.9 28.3 - - + -
285A PHE* 4.4 4.3 - - + -
288A VAL* 3.8 23.6 - - + -
290A LEU 3.0 10.4 + - - +
291A VAL* 4.2 11.7 - - + -
292A LEU* 3.0 31.4 + - - +
359A HIS* 3.6 29.2 - - + -
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Residues in contact with LEU 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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220A VAL* 1.3 71.4 - - - +
222A VAL* 1.3 56.4 + - - +
223A VAL* 3.8 11.8 + - + -
236A ILE* 4.1 22.2 - - + +
239A LEU* 4.5 20.4 - - + -
240A ALA* 4.1 27.1 - - + -
245A ILE* 3.8 21.8 - - + -
246A PRO 2.9 11.2 + - - +
247A VAL* 3.4 5.5 - - + +
248A ILE* 2.8 33.8 + - - +
292A LEU* 3.6 34.5 - - + +
294A VAL* 4.1 12.8 - - + -
342A PHE* 6.5 0.7 - - + -
346A PHE* 5.9 1.8 - - + -
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Residues in contact with VAL 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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220A VAL* 4.0 11.6 - - + -
221A LEU* 1.3 74.0 - - - +
223A VAL* 1.3 64.6 + - - +
224A GLY 3.9 0.3 + - - -
248A ILE* 3.2 18.2 - - + +
250A THR* 5.2 2.5 - - + -
285A PHE* 4.4 12.1 - - + -
291A VAL* 3.8 23.1 - - + -
292A LEU 2.9 10.9 + - - +
293A THR* 3.4 16.4 - - + -
294A VAL 2.8 26.3 + - - +
296A TYR* 5.7 4.4 - - + -
302A LEU* 3.7 35.7 - - + -
307A TRP* 5.3 2.5 - - + -
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Residues in contact with VAL 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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221A LEU* 4.3 11.7 - - + -
222A VAL* 1.3 75.4 - - - +
224A GLY* 1.3 70.4 + - - +
227A ALA* 3.8 18.2 - - + -
228A ILE* 5.4 0.2 - - + -
236A ILE* 4.2 23.6 - - + -
247A VAL* 3.9 25.4 - - + -
248A ILE 2.8 11.8 + - - +
249A THR* 3.5 5.3 - - + -
250A THR* 3.2 25.6 + - - -
253A ALA* 3.3 8.2 - - + +
256A VAL* 4.3 22.7 - - + -
294A VAL* 3.7 11.0 - - + +
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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