Contacts of the strand formed by residues 210 - 216 (chain T) in PDB entry 5A0Q
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 VAL 210 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47T VAL* 4.5 2.7 - - + -
48T ALA 3.6 3.6 - - - -
50T LYS* 5.5 2.0 - - - -
192T LEU* 3.6 31.6 - - + -
195T LEU* 3.0 33.9 - - + -
209T ASN* 1.3 89.9 + - - +
211T SER* 1.4 64.3 + - - +
212T ILE* 4.0 9.0 + - + +
224T TYR 5.1 1.0 - - - +
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Residues in contact with SER 211 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47T VAL* 3.6 1.2 - - - +
48T ALA* 3.1 32.9 + - - +
50T LYS* 3.1 39.8 + - - +
62T LYS 5.0 3.5 + - - -
63T ILE* 3.7 22.4 - - - -
209T ASN 3.9 0.8 - - - -
210T VAL* 1.4 72.5 - - - +
212T ILE* 1.4 65.6 + - - +
223T ILE* 3.9 13.2 - - - -
224T TYR 4.1 4.7 - - - -
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Residues in contact with ILE 212 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45T VAL* 4.9 0.7 - - + -
46T LEU 3.6 11.0 - - - +
47T VAL* 4.2 12.1 - - + -
63T ILE* 3.6 4.3 - - - -
188T VAL* 3.2 35.7 - - + -
192T LEU* 4.1 20.2 - - + -
210T VAL* 4.0 9.8 + - + +
211T SER* 1.4 80.9 - - - +
213T GLY* 1.3 60.8 + - - +
214T ILE* 3.8 26.7 - - + -
223T ILE* 3.6 4.0 - - - +
224T TYR* 2.9 51.8 + - + +
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Residues in contact with GLY 213 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44T ALA 3.8 4.3 - - - +
45T VAL* 3.8 0.9 - - - -
46T LEU* 2.9 40.3 + - - +
63T ILE* 3.4 13.5 - - - +
212T ILE* 1.3 71.3 - - - +
214T ILE* 1.3 62.7 + - - -
221T PHE* 3.8 23.8 - - - -
222T THR 3.3 8.5 - - - -
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Residues in contact with ILE 214 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43T HIS* 3.3 11.4 - - + -
44T ALA 3.6 9.4 - - - +
45T VAL* 3.9 7.4 - - + -
184T LEU* 2.6 70.9 - - + -
188T VAL* 3.8 17.0 - - + -
212T ILE* 3.8 9.4 - - + -
213T GLY* 1.3 77.4 - - - +
215T VAL* 1.3 64.1 + - - +
219T LEU* 3.7 8.0 - - + +
220T GLU 3.5 0.7 - - - +
221T PHE* 3.3 3.0 - - - -
222T THR* 3.1 35.3 + - - +
224T TYR* 3.5 32.7 - - + +
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Residues in contact with VAL 215 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43T HIS* 3.1 10.1 - - - +
44T ALA* 3.0 40.5 + - + -
69T HIS* 3.8 17.5 - - + -
137T TYR* 3.7 36.3 - - + +
214T ILE* 1.3 73.7 - - - +
216T GLY* 1.3 63.1 + - - +
219T LEU* 3.4 15.5 - - - +
220T GLU* 4.0 1.6 - - - -
221T PHE* 3.4 43.3 - - + +
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Residues in contact with GLY 216 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42T THR 3.0 17.9 - - - -
43T HIS* 3.3 8.7 - - - -
137T TYR* 3.4 20.4 - - - -
215T VAL* 1.3 77.4 - - - +
217T LYS* 1.3 63.4 + - - -
218T ASP 3.2 2.9 - - - -
219T LEU 2.9 17.8 + - - +
220T GLU* 5.4 0.9 - - - +
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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