Contacts of the strand formed by residues 219 - 224 (chain A) in PDB entry 4HXG
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 PHE 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A TRP* 3.8 10.6 - - - +
202A ILE* 3.5 11.1 - - + +
214A PHE* 3.8 22.4 - + - -
217A VAL* 3.4 32.0 - - + +
218A SER* 1.3 77.9 - - - +
220A TYR* 1.3 63.0 + - - +
231A LEU* 3.5 39.0 - - + -
232A TYR 3.3 20.9 - - - +
233A GLY* 3.4 11.2 - - - -
234A LYS 3.6 12.8 - - - +
235A PRO* 3.8 25.4 - - + -
247A TYR* 3.9 11.7 - + - -
253A VAL* 4.3 14.8 - - + -
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Residues in contact with TYR 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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175A SER* 5.3 9.6 - - - -
186A SER* 3.5 22.9 - - - +
197A PHE* 6.5 0.2 - + - -
200A TRP* 3.5 46.2 - + + -
202A ILE* 4.0 7.2 - - - -
219A PHE* 1.3 75.3 - - - +
221A ALA* 1.3 69.2 + - - +
222A ILE* 3.4 18.0 + - + +
231A LEU* 3.5 6.0 - - - -
232A TYR* 2.8 60.0 + + - +
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Residues in contact with ALA 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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175A SER* 4.9 5.4 + - - -
177A ILE* 4.1 20.7 - - + +
184A VAL* 3.8 23.6 - - + +
186A SER* 3.2 12.0 + - - +
202A ILE* 4.5 2.8 - - + +
220A TYR* 1.3 79.5 - - - +
222A ILE* 1.3 63.2 + - - +
223A ASP 3.7 0.2 - - - -
229A ILE* 3.8 25.8 - - + -
230A LEU 3.5 6.3 - - - -
231A LEU* 3.8 6.0 - - + +
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Residues in contact with ILE 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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177A ILE* 4.2 9.4 - - - +
220A TYR* 3.7 22.4 - - + +
221A ALA* 1.3 74.7 - - - +
223A ASP* 1.3 66.3 + - - +
230A LEU* 3.0 25.2 + - + +
232A TYR* 3.4 42.0 - - + -
246A ILE* 4.6 0.9 - - + -
267A ALA* 3.7 42.3 - - + +
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Residues in contact with ASP 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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110A GLU* 5.1 6.1 - - - +
177A ILE* 3.3 20.0 - - - +
222A ILE* 1.3 84.4 - - + +
224A SER* 1.3 78.8 + - - +
229A ILE* 3.7 3.8 - - - +
230A LEU* 3.0 32.7 + - + -
267A ALA 4.8 0.4 - - - +
268A LYS* 3.5 16.6 - - - +
269A ILE* 3.0 39.8 + - + +
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Residues in contact with SER 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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177A ILE* 3.9 3.8 - - - +
178A TRP 3.3 25.6 + - - -
179A HIS* 2.8 24.7 + - - -
180A GLY 4.4 0.2 + - - -
223A ASP* 1.3 91.9 + - - +
225A ASP* 1.3 58.1 + - - +
226A GLY* 2.7 26.9 + - - -
228A ARG 3.4 7.2 - - - -
229A ILE* 4.8 1.1 - - - -
269A ILE* 3.8 11.6 - - - +
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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