Contacts of the strand formed by residues 218 - 224 (chain T) in PDB entry 6MZL
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 LYS 218 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171T THR* 6.4 1.3 - - - -
172T VAL 3.3 8.1 - - - +
173T ASN* 3.8 29.6 - - + +
212T LEU 4.2 0.2 - - - +
213T ILE* 5.2 0.4 - - - +
214T PHE* 3.2 47.2 + - + +
216T SER* 3.7 11.0 + - - +
217T GLY* 1.3 78.5 - - - +
219T MET* 1.3 60.6 + - - +
220T VAL* 5.2 2.9 - - + -
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Residues in contact with MET 219 (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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171T THR* 3.3 5.3 - - - -
172T VAL* 2.9 55.3 + - + +
174T LEU* 4.3 23.3 - - + -
211T ALA* 4.2 9.2 - - + -
212T LEU 3.3 16.8 - - - +
213T ILE* 3.6 27.8 - - + -
218T LYS* 1.3 76.6 - - - +
220T VAL* 1.3 64.2 + - - +
221T CYS* 5.5 2.3 - - + +
234T ALA* 3.4 30.3 - - + +
237T TYR* 3.7 22.7 - - + +
238T ALA 3.8 8.7 - - - +
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Residues in contact with VAL 220 (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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41A PHE* 3.5 28.8 - - + -
81A LEU* 3.6 25.8 - - - +
82A THR* 5.6 0.7 - - - -
169T VAL* 4.4 6.3 - - + -
170T SER 3.3 11.9 - - - +
171T THR* 3.8 19.3 - - + -
211T ALA* 3.4 3.3 - - - +
212T LEU* 2.9 41.9 + - + +
214T PHE* 4.8 19.7 - - + -
218T LYS* 5.2 2.0 - - + -
219T MET* 1.3 80.8 - - - +
221T CYS* 1.3 62.4 + - - +
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Residues in contact with CYS 221 (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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41A PHE* 3.8 3.8 - - - -
168T ILE 3.9 1.2 - - - +
169T VAL* 3.2 14.0 - - - +
170T SER* 2.8 46.5 + - - +
209T THR* 4.7 2.5 - - - -
210T THR 3.8 5.4 - - - -
211T ALA* 4.5 3.6 - - + +
219T MET* 5.5 2.9 - - + +
220T VAL* 1.3 74.9 - - - +
222T THR* 1.3 72.7 + - - +
224T ALA 5.8 0.2 - - - -
230T SER* 4.1 25.6 - - - -
233T ALA* 4.4 16.8 - - - -
234T ALA* 4.6 12.8 - - + -
237T TYR* 5.0 5.2 - - - -
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Residues in contact with THR 222 (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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41A PHE* 3.1 61.1 - - + +
45A ASN* 4.1 15.7 - - - +
46A ILE 4.1 2.0 + - - +
167T ASN* 4.0 7.0 - - - +
168T ILE 4.4 1.3 - - - -
169T VAL* 4.6 0.2 - - + -
209T THR* 3.2 11.6 - - - +
210T THR* 2.4 61.8 + - - +
221T CYS* 1.3 73.4 - - - +
223T GLY* 1.3 59.8 + - - +
224T ALA 3.6 2.7 - - - -
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Residues in contact with GLY 223 (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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44A GLY* 5.2 0.7 - - - -
45A ASN* 3.3 36.2 + - - -
55A GLU* 5.5 1.6 - - - +
166T GLN 4.6 4.2 - - - +
167T ASN* 3.0 15.4 + - - -
207T PRO* 6.0 0.2 - - - +
208T ARG 3.7 14.0 - - - +
209T THR* 4.0 0.9 - - - -
222T THR* 1.3 74.2 - - - +
224T ALA* 1.3 63.7 + - - +
225T LYS* 3.8 10.2 + - - +
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Residues in contact with ALA 224 (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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167T ASN* 3.3 8.1 + - - -
168T ILE* 2.9 29.8 + - + +
207T PRO* 5.3 1.3 - - - -
209T THR* 3.8 10.7 - - + +
221T CYS* 5.9 0.2 - - - -
222T THR 3.6 2.4 - - - -
223T GLY* 1.3 77.1 - - - +
225T LYS* 1.3 59.7 + - - +
226T SER 3.5 8.5 - - - +
229T GLN* 3.8 11.4 - - + -
230T SER* 3.4 42.0 - - - +
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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