Contacts of the strand formed by residues 222 - 229 (chain D) in PDB entry 6NR8
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 GLU 222 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186D MET* 4.8 2.9 - - - -
220D ASP 4.3 3.5 - - - +
221D CYS* 1.3 75.8 - - - +
223D LEU* 1.3 72.3 + - - +
224D VAL* 4.0 22.5 - - + +
375D LYS* 5.9 0.3 - - - -
388D ILE* 3.3 6.2 - - - +
389D VAL* 2.9 29.2 + - + +
391D ARG* 3.7 23.7 + - - +
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Residues in contact with LEU 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186D MET* 3.3 39.0 - - + +
189D ASN* 5.6 2.0 - - + -
190D ALA* 3.7 15.5 - - + +
193D LYS* 5.5 4.5 - - - +
222D GLU* 1.3 83.9 - - - +
224D VAL* 1.3 63.4 + - - +
225D GLU* 4.1 14.5 + - - +
386D VAL* 3.7 22.7 - - + -
387D THR 3.4 15.3 - - - +
388D ILE* 3.7 32.1 - - + -
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Residues in contact with VAL 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222D GLU* 4.0 22.1 + - + +
223D LEU* 1.3 76.5 - - - +
225D GLU* 1.3 75.4 + - - +
228D VAL* 3.7 23.0 - - + +
375D LYS* 4.0 28.3 - - + -
376D ILE 5.0 0.7 - - - +
377D THR* 4.8 11.4 - - + -
387D THR* 2.8 33.4 + - - +
389D VAL* 3.8 20.0 - - + -
391D ARG* 5.5 0.2 - - - +
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Residues in contact with GLU 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D LYS* 3.3 34.2 + - - +
223D LEU* 4.5 11.5 - - - +
224D VAL* 1.3 85.0 - - - +
226D GLY* 1.3 66.0 + - - +
227D LEU* 3.5 1.4 + - - +
376D ILE 2.9 17.8 - - - +
377D THR* 5.3 1.5 - - - +
378D GLY* 3.6 15.8 + - - +
384D LYS* 3.3 29.9 - - - +
385D THR 3.4 12.1 - - - +
386D VAL* 3.6 21.6 - - - +
387D THR 4.8 0.2 - - - +
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Residues in contact with GLY 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D GLU* 1.3 75.3 - - - +
227D LEU* 1.3 56.1 + - - -
340D ILE* 4.6 7.4 - - - -
376D ILE* 3.7 6.7 - - - -
378D GLY* 4.1 13.4 - - - +
379D CYS* 4.7 2.7 - - - -
381D SER* 5.3 0.4 - - - -
385D THR* 2.9 35.4 + - - +
387D THR* 2.5 25.3 + - - -
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Residues in contact with LEU 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D ASP 4.9 0.2 - - - +
209D LYS* 3.7 25.8 - - + +
225D GLU 3.5 0.6 + - - +
226D GLY* 1.3 76.9 - - - +
228D VAL* 1.3 65.3 + - - +
229D LEU* 4.1 3.6 - - + -
335D PHE* 3.8 15.5 - - + -
336D ILE* 3.7 37.0 - - + -
339D THR* 3.3 21.3 - - - +
340D ILE* 3.8 13.0 - - + +
376D ILE* 3.3 45.6 + - + +
385D THR* 3.7 15.9 - - + -
387D THR* 3.4 17.0 - - - +
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Residues in contact with VAL 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D LYS* 2.9 25.5 + - - +
211D VAL* 3.6 33.4 - - + +
224D VAL* 3.7 35.7 - - + -
227D LEU* 1.3 76.9 - - - +
229D LEU* 1.3 66.6 + - - +
230D THR* 4.3 1.0 + - - +
373D LEU* 4.1 7.0 - - + -
374D LEU 3.4 14.1 - - - +
375D LYS* 3.8 18.2 - - + -
387D THR* 3.8 18.4 - - + +
389D VAL* 3.9 9.9 - - + -
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Residues in contact with LEU 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D LYS* 4.3 15.9 - - - +
211D VAL* 5.8 0.2 - - - -
227D LEU* 4.1 3.8 + - + -
228D VAL* 1.3 74.8 - - - +
230D THR* 1.3 64.1 + - - +
297D VAL* 4.7 5.4 - - + -
299D LEU* 4.4 10.8 - - + -
325D ILE* 3.9 30.1 - - + -
328D ILE* 4.3 21.8 - - + -
336D ILE* 4.5 11.4 - - + -
373D LEU* 3.4 12.9 - - - +
374D LEU* 2.8 54.3 + - + +
376D ILE* 3.8 30.7 - - + -
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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