Contacts of the strand formed by residues 220 - 224 (chain A) in PDB entry 7EHI
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 ASP 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A PHE* 3.5 14.6 - - - +
209A GLN* 3.2 29.0 + - + +
218A THR* 3.7 3.3 - - - +
219A GLN* 1.3 80.7 - - + +
221A TYR* 1.3 64.5 + - - +
222A MET* 2.9 23.3 + - - +
223A THR* 2.9 31.3 + - - +
325A TYR* 5.6 2.4 + - - -
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Residues in contact with TYR 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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208A PHE* 3.6 24.5 - + + -
218A THR* 3.7 25.9 - - + -
219A GLN 5.8 0.2 - - - -
220A ASP* 1.3 73.9 + - - +
222A MET* 1.3 58.9 + - + +
223A THR 3.4 0.9 - - - -
253A VAL* 2.8 36.6 + - + -
254A PHE* 4.2 20.6 - + - -
256A HIS 3.1 14.7 + - - -
257A ILE* 3.7 28.1 - - + +
315A LEU* 3.9 8.4 - - + +
325A TYR* 3.3 33.5 + + - +
326A LEU* 5.0 1.8 - - + -
329A ILE* 3.5 31.6 - - + -
333A TRP* 2.9 28.4 + - - -
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Residues in contact with MET 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 ASP* 2.9 13.4 + - - +
221A TYR* 1.3 81.8 - - + +
223A THR* 1.3 61.4 + - - +
325A TYR* 6.0 3.6 - - + -
328A ASN* 5.0 1.3 - - - +
329A ILE* 4.0 28.3 - - + -
332A TYR* 3.5 65.1 + - + -
333A TRP* 3.8 11.8 - - - -
606A SO4 5.8 0.2 + - - -
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Residues in contact with THR 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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208A PHE* 3.3 6.7 - - - -
209A GLN* 2.9 39.3 + - + +
220A ASP* 2.9 26.3 + - - +
221A TYR 3.4 1.6 + - - -
222A MET* 1.3 80.8 + - - +
224A VAL* 1.3 74.9 + - - +
226A PRO* 5.2 3.8 - - + -
333A TRP* 4.4 4.3 - - - -
606A SO4 4.2 23.0 + - - +
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Residues in contact with VAL 224 (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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184A LEU* 3.9 19.1 - - + -
207A ILE* 3.6 18.8 - - + +
208A PHE* 4.4 0.7 - - - +
223A THR* 1.3 87.1 - - - +
225A ASP* 1.3 79.6 + - - +
226A PRO* 3.1 3.5 - - - +
228A PHE* 4.2 3.8 - - + -
229A GLY 3.6 25.2 - - - +
230A ASP* 4.0 21.1 - - - +
231A ALA* 4.4 3.3 - - - +
234A PHE* 4.1 13.0 - - + -
333A TRP* 3.8 27.6 - - + -
606A SO4 4.5 3.8 + - - -
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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