Contacts of the strand formed by residues 217 - 222 (chain N) in PDB entry 7K63
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 217 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197N ILE* 3.8 15.5 - - + -
209N TYR* 3.6 19.8 - - + -
213N PHE* 2.9 21.0 + - + +
215N GLY 4.0 7.8 + - - -
216N LYS* 1.3 77.4 - - - +
218N THR* 1.3 69.1 + - - +
219N LEU* 5.6 1.3 - - + -
230N MET* 3.6 31.4 - - + -
231N GLU 3.5 4.0 - - - -
232N LEU* 4.6 2.0 - - + -
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Residues in contact with THR 218 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209N TYR* 3.6 11.9 + - - +
215N GLY* 4.4 7.8 + - - -
217N ALA* 1.3 81.3 + - - +
219N LEU* 1.3 69.4 + - - +
220N THR* 4.2 10.0 + - + +
229N TYR 3.8 1.9 - - - +
230N MET* 4.9 0.4 - - - +
231N GLU* 3.1 53.3 + - + +
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Residues in contact with LEU 219 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185N TRP* 3.4 33.9 - - + +
197N ILE* 5.6 2.5 - - + -
198N GLY* 3.9 6.7 - - - +
199N TYR* 3.6 40.8 - - - +
200N ILE* 3.8 21.4 - - + +
207N THR* 4.1 5.6 - - + +
209N TYR* 3.0 33.7 + - + +
217N ALA* 5.6 1.3 - - + -
218N THR* 1.3 76.7 - - - +
220N THR* 1.3 69.1 + - - +
228N VAL* 4.7 2.9 - - + -
229N TYR 3.3 3.1 - - - +
230N MET* 3.6 26.7 - - + -
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Residues in contact with THR 220 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168N LYS* 4.4 9.7 + - - +
200N ILE* 3.5 5.8 - - - -
218N THR* 4.9 12.8 - - + +
219N LEU* 1.3 79.7 - - - +
221N SER* 1.3 62.4 + - - +
228N VAL* 3.4 6.8 - - - +
229N TYR* 2.7 59.9 + - - +
231N GLU* 6.3 1.6 - - + -
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Residues in contact with SER 221 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178N PHE* 4.6 2.9 - - - -
200N ILE* 3.7 19.4 - - - +
202N PRO* 4.4 23.0 + - - +
205N ALA* 4.7 9.7 - - - +
220N THR* 1.3 77.9 - - - +
222N ASP* 1.3 60.6 + - - +
223N LYS* 4.1 6.8 + - - +
227N THR 3.5 7.6 - - - -
228N VAL* 4.2 11.2 - - - +
229N TYR* 5.3 2.7 - - - -
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Residues in contact with ASP 222 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178N PHE* 4.0 2.3 - - - -
221N SER* 1.3 75.5 - - - +
223N LYS* 1.3 57.6 + - - +
224N SER* 2.5 31.2 + - - -
225N SER* 2.9 24.9 + - - +
226N SER* 2.9 24.8 + - - -
227N THR 2.7 18.4 + - - +
229N TYR* 4.4 16.2 + - + -
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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