Contacts of the strand formed by residues 220 - 226 (chain D) in PDB entry 4G5S
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 ALA 220 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D LYS 3.2 4.8 + - - +
36D LEU* 3.3 24.7 - - + +
37D LEU 3.2 20.8 + - - -
218D VAL* 3.6 3.1 - - - +
219D THR* 1.3 83.8 - - + +
221D ILE* 1.3 64.5 + - - +
262D THR* 3.7 2.0 - - - -
263D SER* 3.2 24.0 - - - +
265D ILE* 4.3 12.3 - - + -
343D ILE* 4.7 11.0 - - + -
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Residues in contact with ILE 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D LEU* 3.5 19.5 - - + +
39D LEU* 4.0 19.3 - - + -
218D VAL* 4.3 9.4 - - + -
220D ALA* 1.3 78.7 - - - +
222D ILE* 1.3 66.8 + - - +
223D PHE* 4.3 6.1 - - + +
253D ILE* 4.1 11.7 - - + -
259D PHE* 3.6 48.5 - - + -
262D THR* 4.1 9.2 - - + -
263D SER 2.9 9.1 + - - -
264D ILE* 3.8 21.4 - - + +
265D ILE* 2.8 35.2 + - - +
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Residues in contact with ILE 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D LEU* 4.3 28.5 - - + -
37D LEU 2.8 11.1 + - - +
38D LEU* 3.5 30.3 - - + +
39D LEU 3.0 25.5 + - - +
49D ILE* 5.8 2.5 - - + -
198D MET* 5.3 3.6 - - - -
221D ILE* 1.3 76.3 - - - +
223D PHE* 1.3 58.8 + - - +
224D CYS* 3.7 3.0 + - - -
265D ILE* 3.4 23.3 - - + +
267D PHE* 3.7 48.9 - - + -
336D PHE* 4.8 12.8 - - + -
339D VAL* 4.9 3.4 - - + -
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Residues in contact with PHE 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D LEU* 3.3 6.7 - - + +
40D GLY* 4.0 14.8 - - - -
221D ILE* 3.9 6.7 + - + +
222D ILE* 1.3 71.7 - - - +
224D CYS* 1.3 66.0 + - - +
225D VAL* 3.5 29.4 - - + -
246D SER* 3.3 34.1 - - - -
249D LEU* 3.6 21.8 - - + -
250D PHE* 3.4 39.7 - + + -
253D ILE* 3.5 35.2 - - + -
264D ILE* 5.6 1.1 - - + -
265D ILE 2.8 10.8 + - - +
266D LEU* 3.7 5.9 - - + +
267D PHE* 2.8 28.1 + - - +
307D PHE* 4.2 0.9 - + - -
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Residues in contact with CYS 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D LEU* 4.2 14.1 - - - -
39D LEU 2.7 17.9 + - - +
40D GLY* 3.5 16.5 - - - -
41D ALA 4.2 0.3 + - - -
44D SER* 3.4 37.6 - - - +
46D LYS* 4.1 14.4 - - - -
49D ILE* 4.6 13.2 - - - -
222D ILE* 4.1 9.0 - - - -
223D PHE* 1.3 79.1 - - - +
225D VAL* 1.3 65.7 + - - +
246D SER* 4.1 2.9 + - - -
267D PHE* 3.6 17.9 - - + +
269D ASN* 5.3 0.9 - - + -
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Residues in contact with VAL 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D SER* 4.5 1.8 - - - -
223D PHE* 3.5 24.7 - - + -
224D CYS* 1.3 80.9 - - - +
226D ALA* 1.3 67.3 + - - +
227D LEU* 3.3 6.5 + - + +
243D MET* 3.8 28.5 - - - -
246D SER* 4.0 9.0 - - - +
266D LEU* 3.9 10.5 - - + -
267D PHE 2.9 12.2 + - - +
268D LEU* 3.6 12.3 - - + -
269D ASN* 2.7 32.6 + - - -
307D PHE* 3.5 25.1 - - + -
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Residues in contact with ALA 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D GLU 3.3 22.4 - - - +
44D SER* 4.2 9.0 - - - +
225D VAL* 1.3 73.7 - - - +
227D LEU* 1.3 64.5 + - - +
229D ASP* 3.2 38.5 + - - +
243D MET* 3.6 8.5 - - - +
246D SER* 5.4 0.6 + - - -
269D ASN* 4.0 4.9 - - - -
270D LYS* 3.7 19.5 - - + -
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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