Contacts of the strand formed by residues 210 - 217 (chain J) in PDB entry 2NX5
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 HIS 210 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163J TRP 3.8 1.2 + - - +
164J VAL* 3.5 10.2 - - - +
165J ASN* 3.1 39.0 + - - +
166J GLY 5.9 1.2 + - - -
208J ARG 4.0 0.4 + - - -
209J ASN* 1.3 72.8 - - - +
211J PHE* 1.3 67.8 + - - +
212J ARG* 3.8 26.2 - - + +
241J GLU* 2.9 45.9 + - + +
242J ALA 3.9 4.5 - - - -
243J TRP* 3.4 44.0 - + + -
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Residues in contact with PHE 211 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J VAL* 5.5 1.1 - - + +
146J LEU* 3.6 31.9 - - + -
162J TRP* 5.0 4.9 - - + -
163J TRP 3.7 2.0 - - - -
164J VAL* 4.0 20.6 - - + -
197J LEU* 4.1 6.3 - - + -
199J VAL* 4.1 13.0 - - + -
203J PHE* 3.6 38.8 - + - -
204J TRP* 3.3 44.9 - + - -
209J ASN* 4.1 21.8 - - + -
210J HIS* 1.3 74.9 - - - +
212J ARG* 1.3 61.6 + - - +
241J GLU* 3.3 4.9 - - - +
242J ALA* 2.9 40.9 + - + +
244J GLY* 4.2 6.3 - - - -
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Residues in contact with ARG 212 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J VAL* 5.8 0.2 - - - -
161J SER 4.0 0.2 - - - +
162J TRP* 3.3 11.1 - - - -
163J TRP* 2.6 90.9 + - + +
166J GLY* 5.4 4.9 - - - -
210J HIS* 3.8 20.6 + - + +
211J PHE* 1.3 74.6 - - - +
213J CYS* 1.3 65.9 + - - +
214J GLN* 3.0 38.0 + - - +
237J ILE* 5.4 1.0 - - - +
239J SER* 4.4 17.3 + - - -
240J ALA 3.8 9.4 - - - +
241J GLU* 4.8 4.5 - - + -
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Residues in contact with CYS 213 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128J VAL* 3.9 2.6 - - - +
130J VAL* 4.1 8.7 - - + -
148J CYS* 2.0 53.4 - - + -
160J LEU* 3.8 25.6 - - - -
161J SER 3.8 3.4 - - - -
162J TRP* 4.0 15.4 - - + -
212J ARG* 1.3 73.0 - - - +
214J GLN* 1.3 60.2 + - - +
215J VAL* 4.3 4.5 - - - -
239J SER* 3.3 24.1 - - - -
240J ALA 3.1 10.8 + - - -
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Residues in contact with GLN 214 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159J GLU 3.6 1.8 + - - +
160J LEU* 3.3 4.2 - - - +
161J SER* 2.9 47.2 + - - +
163J TRP* 3.8 24.2 - - + +
212J ARG* 3.0 38.1 + - - +
213J CYS* 1.3 71.3 - - - +
215J VAL* 1.3 67.0 + - - +
216J GLN* 4.6 5.8 - - - +
237J ILE* 3.6 41.6 - - + +
239J SER* 3.9 5.4 - - - -
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Residues in contact with VAL 215 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126J PRO* 3.9 22.2 - - + -
128J VAL* 3.6 20.6 - - + -
150J ALA* 4.1 11.7 - - + -
158J VAL* 4.0 24.2 - - + -
159J GLU 3.4 4.9 - - - +
160J LEU* 3.8 28.0 - - + +
193J LEU* 6.0 0.7 - - + -
213J CYS* 4.3 7.4 - - - -
214J GLN* 1.3 80.3 - - - +
216J GLN* 1.3 62.9 + - - +
217J PHE* 3.7 2.8 + - - +
236J GLN 4.0 0.2 - - - +
237J ILE* 3.7 0.7 - - - -
238J VAL* 3.0 38.0 + - - +
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Residues in contact with GLN 216 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157J HIS 4.0 0.2 - - - +
158J VAL* 3.1 8.5 - - - +
159J GLU* 2.8 47.0 + - + +
214J GLN* 4.1 7.8 - - - +
215J VAL* 1.3 72.3 - - - +
217J PHE* 1.3 83.6 + - - +
218J TYR* 3.7 32.7 - - + +
235J THR* 3.4 17.8 - - - +
236J GLN* 2.9 20.2 + - - +
237J ILE* 3.3 26.2 - - + +
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Residues in contact with PHE 217 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123J VAL* 3.9 7.4 - - + -
124J PHE 3.2 28.3 - - - -
125J PRO* 4.2 10.8 - - + -
126J PRO* 3.6 30.5 - - + -
153J PHE* 4.1 8.5 - - + -
154J PHE 3.4 17.0 - - - -
155J PRO* 3.9 15.0 - - + -
157J HIS 3.7 11.7 - - - -
158J VAL* 4.2 3.6 - - + -
215J VAL 3.7 0.9 + - - +
216J GLN* 1.3 92.3 + - - +
218J TYR* 1.3 69.0 + - - +
219J GLY* 3.4 21.5 - - - -
233J PRO 3.9 11.2 - - - -
234J VAL 4.0 12.6 - - - -
235J THR* 3.3 4.2 - - - -
236J GLN* 3.0 28.4 + - + +
238J VAL* 5.9 0.2 - - + -
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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