Contacts of the strand formed by residues 217 - 223 (chain B) in PDB entry 6Q0R
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 MET 217 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126B VAL* 3.7 26.0 - - - -
127B ARG* 3.4 29.6 - - + +
128B LEU* 5.3 0.9 - - - -
130B GLN* 4.7 4.9 - - + -
184B THR 3.3 4.9 - - - -
185B VAL* 3.9 28.5 - - + -
216B PHE* 1.3 76.0 - - - +
218B LEU* 1.3 62.7 + - - +
219B HIS* 3.5 24.7 - - + +
419C VAL* 3.5 8.0 - - - +
420C THR* 2.8 39.4 + - + +
421C ASP 3.6 23.8 - - - +
422C LEU* 4.4 12.6 - - - +
423C ARG 5.5 1.6 - - - +
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Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B VAL* 5.6 0.9 - - + +
183B SER* 3.0 9.7 - - - -
184B THR* 2.8 54.3 + - - +
216B PHE* 4.7 2.9 - - + -
217B MET* 1.3 74.3 - - - +
219B HIS* 1.3 66.7 + - - +
220B THR* 5.0 4.0 - - + -
254B CYS* 6.2 0.9 - - + -
256B VAL* 3.7 23.1 - - + -
417C PHE* 3.6 37.2 - - + -
418C VAL 4.3 0.2 - - - -
419C VAL* 4.1 25.1 - - + +
441C LEU* 4.6 0.2 - - + -
443C VAL* 3.6 31.4 - - + -
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Residues in contact with HIS 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ARG 3.9 2.7 - - - -
128B LEU* 4.3 0.4 - - - -
129B PHE* 3.4 23.0 + - + -
130B GLN* 3.5 29.1 - - + +
132B GLU* 6.4 1.1 - - + -
182B VAL 3.6 3.6 - - - -
183B SER* 2.7 27.4 + - - +
217B MET* 3.5 32.4 - - + +
218B LEU* 1.3 78.0 + - - +
220B THR* 1.3 65.3 + - - +
416C PRO 3.7 0.2 - - - +
417C PHE* 3.4 6.4 - - - -
418C VAL* 2.9 61.5 + - + +
420C THR* 3.4 21.3 - - + +
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Residues in contact with THR 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B PHE* 5.5 1.2 - - - -
181B TYR* 3.6 4.2 - - - +
182B VAL* 3.0 64.4 + - + +
218B LEU* 5.0 3.8 - - + -
219B HIS* 1.3 76.6 - - - +
221B LYS* 1.3 64.5 + - - +
222B TYR* 4.9 1.3 - - + -
245B LEU* 4.7 9.6 - - + -
254B CYS* 5.9 0.2 - - - -
415C LEU* 3.9 21.4 - - + +
416C PRO 3.0 20.1 + - - -
417C PHE* 3.8 19.3 - - + -
418C VAL* 5.8 1.3 - - - -
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Residues in contact with LYS 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B GLU* 4.3 17.0 - - + +
179B ASP* 6.5 0.2 - - + -
180B ILE 3.3 10.3 - - - +
181B TYR* 4.1 23.1 - - + -
220B THR* 1.3 76.5 + - - +
222B TYR* 1.3 64.5 + - - +
415C LEU* 4.3 0.2 - - - +
416C PRO* 4.0 23.8 + - + +
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Residues in contact with TYR 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B PHE* 5.7 0.2 - - - -
178B ARG 3.7 1.2 - - - +
179B ASP* 3.9 1.7 - - - -
180B ILE* 3.0 65.4 + - + +
182B VAL* 3.9 17.7 - - + -
220B THR* 4.9 1.8 - - - -
221B LYS* 1.3 75.8 - - - +
223B GLN* 1.4 62.6 + - - +
224B VAL* 3.6 19.1 - - + -
236B GLN* 5.2 1.7 + - - -
245B LEU* 3.4 37.8 - - + +
246B ASN 3.3 27.0 + - - -
247B THR* 3.8 17.5 - - + -
415C LEU* 3.7 28.9 - - + -
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Residues in contact with GLN 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B SER* 3.2 15.1 + - - -
177B HIS* 3.5 35.5 + - - +
178B ARG 3.4 4.9 - - - +
179B ASP* 3.0 25.6 - - - +
222B TYR* 1.4 73.8 - - - +
224B VAL* 1.3 61.7 + - - +
225B VAL* 5.3 0.3 - - - +
247B THR* 3.8 13.9 - - - +
248B SER* 4.3 0.9 + - - -
249B TYR* 4.4 9.5 - - - -
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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
------------------------------------------------------------
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