Contacts of the helix formed by residues 220 - 225 (chain B) in PDB entry 4D87
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 THR 220 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ILE* 5.3 3.0 - - - +
139B ILE 4.2 7.6 - - - +
140B ASP* 4.3 2.2 - - - -
141B GLU* 4.1 28.7 - - + +
214B GLN* 3.3 14.9 - - + +
217B VAL* 2.6 34.2 - - + +
218B VAL 2.2 11.3 + - - -
219B PRO* 1.3 76.9 - - + +
221B ALA* 1.3 49.4 + - - -
222B PRO* 2.6 5.5 - - - +
223B ASN* 2.5 56.2 + - - +
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Residues in contact with ALA 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B HIS* 4.0 1.1 - - + -
208B HIS* 3.7 14.6 - - + +
214B GLN 2.6 21.7 + - - +
215B MET* 3.8 4.7 - - - +
218B VAL* 1.9 43.8 + - - +
220B THR* 1.3 64.9 + - - +
222B PRO* 1.3 66.6 - - + +
223B ASN 3.0 1.7 + - - -
224B ASP* 3.3 10.4 + - - +
227B PHE* 3.4 33.8 - - + +
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Residues in contact with PRO 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B TYR* 3.6 24.1 + - - -
38B TYR 3.9 13.9 - - - +
39B ILE* 3.9 13.7 - - + +
42B HIS* 2.9 51.1 - - + +
72B TYR* 3.9 4.3 - - - +
219B PRO 3.4 6.7 - - - +
220B THR 2.6 6.7 - - - -
221B ALA* 1.3 87.8 - - + +
223B ASN* 1.3 62.4 + - - -
224B ASP 3.0 3.1 + - - +
227B PHE* 3.8 17.7 - - + -
228B PHE* 4.0 7.6 - - + -
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Residues in contact with ASN 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ILE* 3.7 21.3 - - - +
136B TRP* 3.1 32.7 + - - -
138B THR* 1.7 45.4 - - + +
139B ILE* 2.7 34.3 + - - +
149B LEU* 4.8 1.0 - - + +
214B GLN* 4.0 16.6 - - + +
220B THR* 2.5 38.7 + - - +
222B PRO* 1.3 72.3 - - - +
224B ASP* 1.3 59.5 + - + +
225B PRO* 3.5 2.1 - - - +
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Residues in contact with ASP 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B TYR* 4.4 0.2 + - - -
149B LEU* 3.6 25.3 - - + +
150B LYS 4.8 0.3 - - - +
151B ARG* 3.1 38.0 + - - +
211B VAL* 4.4 2.3 - - - +
214B GLN* 5.1 2.7 - - + -
215B MET* 3.9 22.8 - - + +
221B ALA 3.3 1.9 + - - +
222B PRO 3.0 3.8 - - - +
223B ASN* 1.3 79.9 - - + +
225B PRO* 1.4 75.4 - - - +
226B VAL* 3.2 22.8 + - - +
227B PHE* 2.9 25.1 + - - +
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Residues in contact with PRO 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B PHE* 5.6 3.6 - - + -
26B VAL* 5.0 7.0 - - + -
35B TYR* 3.7 12.6 - - - +
114B MET* 3.9 18.6 - - + -
131B PHE* 3.3 46.0 - - + -
136B TRP* 4.1 10.8 - - + -
149B LEU* 4.1 10.5 - - + -
151B ARG* 4.6 0.4 - - - +
223B ASN 3.5 8.3 - - - +
224B ASP* 1.4 91.5 - - - +
226B VAL* 1.3 55.0 + - - +
228B PHE* 3.1 28.8 + - - +
229B LEU* 3.9 5.5 + - - +
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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