Contacts of the strand formed by residues 221 - 228 (chain A) in PDB entry 2DFS
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 GLY 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A PHE* 1.3 81.2 - - - +
222A LYS* 1.3 60.9 + - - -
240A ARG 4.0 0.2 - - - +
241A THR* 3.5 2.3 - - - -
242A TYR* 2.9 41.3 + - - -
243A LEU* 4.5 3.4 - - - +
436A LEU* 4.7 4.7 - - - -
437A ASP 3.6 8.1 - - - -
438A ILE* 4.4 18.4 - - - -
439A TYR* 4.7 0.4 - - - -
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Residues in contact with LYS 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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170A THR* 4.7 7.4 - - - +
199A SER* 6.1 0.7 - - - -
200A ASN* 2.8 28.8 + - - +
203A MET* 4.3 24.3 - - + +
204A GLU* 4.9 7.9 + - - +
220A PHE* 3.7 30.1 + - + -
221A GLY* 1.3 70.7 - - - -
223A TYR* 1.3 61.5 + - - +
224A ILE* 4.1 28.4 - - + +
239A MET* 4.4 9.9 - - + -
240A ARG 3.7 2.9 - - - +
435A VAL 3.6 2.3 - - - +
436A LEU* 3.6 2.2 - - - +
437A ASP* 2.9 60.4 + - + +
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Residues in contact with TYR 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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157A GLN 4.0 0.2 + - - -
158A SER* 2.8 27.4 + - - -
221A GLY 4.2 0.2 - - - -
222A LYS* 1.3 73.7 - - - +
224A ILE* 1.3 61.4 + - - +
225A GLU* 3.5 35.6 + - + -
238A ASN 3.6 1.7 - - - +
239A MET* 3.4 3.3 - - - -
240A ARG* 2.8 51.7 + - + +
242A TYR* 4.1 16.8 - + + -
432A PHE* 3.7 16.4 - + - -
434A GLY* 3.6 29.9 - - - -
435A VAL 3.4 15.7 - - - -
436A LEU* 3.7 21.1 - - + -
647A LEU* 5.6 1.1 - - + -
650A THR* 3.8 21.8 + - + +
651A LEU* 4.2 10.8 - - + +
654A THR* 4.4 2.1 - - - +
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Residues in contact with ILE 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 MET* 5.0 4.9 - - - -
196A VAL* 4.2 26.0 - - + -
199A SER* 5.3 0.7 - - - +
222A LYS* 4.1 21.3 - - + +
223A TYR* 1.3 72.0 - - - +
225A GLU* 1.3 60.1 + - - +
226A ILE* 3.8 25.0 + - + +
237A ALA* 4.1 11.9 - - + -
238A ASN 3.4 6.3 - - - +
239A MET* 3.7 43.3 - - + -
423A LEU* 4.9 2.7 - - + -
433A ILE 3.9 0.7 - - - +
434A GLY* 3.3 1.2 - - - -
435A VAL* 2.8 43.9 + - + +
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Residues in contact with GLU 225 (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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223A TYR* 3.5 33.7 - - + +
224A ILE* 1.3 69.9 - - - +
226A ILE* 1.3 61.0 + - - +
227A GLY* 3.7 0.6 + - - -
237A ALA* 3.1 7.1 - - - +
238A ASN* 2.7 61.8 + - + +
240A ARG* 2.6 49.1 + - - -
429A GLN* 6.1 0.9 - - - +
432A PHE* 4.0 30.4 - - + -
433A ILE 3.9 3.8 - - - -
434A GLY* 3.9 2.2 - - - -
650A THR* 4.3 4.0 - - - +
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Residues in contact with ILE 226 (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 MET* 4.3 26.2 - - + -
180A PHE* 5.1 14.4 - - + -
192A VAL* 6.0 4.5 - - + -
196A VAL* 5.4 1.3 - - + -
224A ILE* 3.8 29.8 - - + +
225A GLU* 1.3 70.9 - - - +
227A GLY* 1.4 58.9 + - - +
228A PHE* 3.3 29.0 - - + -
234A ILE* 4.2 16.8 - - + -
236A GLY 3.9 7.0 - - - +
237A ALA* 4.0 9.2 - - + -
432A PHE* 3.1 5.9 - - - -
433A ILE* 2.8 43.3 + - + +
435A VAL* 5.1 6.3 - - + -
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Residues in contact with GLY 227 (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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225A GLU 3.7 3.0 + - - -
226A ILE* 1.4 72.1 - - - +
228A PHE* 1.3 61.3 + - - -
233A ARG 3.8 0.5 - - - +
234A ILE* 3.9 2.8 - - - -
235A ILE* 3.1 34.2 + - - +
236A GLY 2.9 19.3 + - - +
237A ALA* 4.4 0.4 - - - +
429A GLN* 3.3 27.4 - - - -
431A SER 3.7 0.4 - - - -
432A PHE* 4.3 0.7 - - - -
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Residues in contact with PHE 228 (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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147A TYR* 4.0 22.2 - + - -
150A MET* 4.0 12.6 - - - -
180A PHE* 4.4 14.4 - + + -
184A SER* 4.5 3.6 - - - -
226A ILE* 3.3 39.5 - - + -
227A GLY* 1.3 71.9 - - - -
229A ASP* 1.4 52.4 + - - +
232A TYR* 3.7 26.9 - + + -
233A ARG 3.5 22.0 - - - +
234A ILE* 3.6 23.8 - - + -
235A ILE* 4.3 4.5 - - - -
429A GLN* 3.6 1.7 - - - +
430A HIS* 2.7 29.9 + - - +
431A SER 2.8 23.5 + - - +
432A PHE* 4.1 1.3 - - - -
433A ILE* 3.9 24.0 - - + -
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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