Contacts of the strand formed by residues 217 - 222 (chain A) in PDB entry 3NUI
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 ILE 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A LYS* 2.9 29.7 + - - -
142A LYS* 3.6 20.4 - - + +
144A LEU* 3.8 31.4 - - + -
177A VAL* 6.4 0.2 - - + -
208A THR 4.7 0.4 - - - +
209A ILE* 4.0 29.4 - - + -
212A GLU* 4.0 17.3 - - + -
213A GLY 3.8 16.4 - - - +
214A ALA* 3.2 8.8 + - - +
215A ASP 3.4 1.0 - - - -
216A THR* 1.3 83.9 - - - +
218A ALA* 1.3 62.6 - - - +
219A GLY 3.9 2.2 - - - +
251A ILE* 3.7 32.9 - - + +
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Residues in contact with ALA 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A LEU* 3.8 10.9 - - + +
129A TRP* 4.0 8.3 - - + -
132A HIS* 2.9 34.5 + - + -
140A LYS 3.3 20.9 - - - +
141A ARG* 3.6 12.7 - - - +
142A LYS 2.7 17.9 + - - +
143A ILE* 3.9 9.9 - - + -
217A ILE* 1.3 72.5 - - - +
219A GLY* 1.3 55.3 + - - +
252A PRO* 3.4 13.4 - - - +
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Residues in contact with GLY 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A LEU* 4.3 11.9 - - - -
142A LYS 3.5 1.9 + - - +
143A ILE* 3.5 11.0 - - - +
144A LEU* 2.8 33.6 + - - +
217A ILE* 3.4 3.6 - - - +
218A ALA* 1.3 81.9 - - - +
220A PHE* 1.3 54.4 + - - +
221A PHE* 4.6 2.2 - - - -
251A ILE* 3.7 8.9 - - - +
252A PRO 3.4 12.8 - - - -
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Residues in contact with PHE 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LEU* 3.3 27.6 - - + -
146A ARG* 3.9 18.6 - - - -
179A LEU* 3.8 22.9 - - + -
205A LEU* 5.5 0.7 - - + -
219A GLY* 1.3 73.7 - - - +
221A PHE* 1.3 61.3 + - - +
222A ALA* 3.5 31.2 - - + -
238A TYR* 4.0 2.0 - - - -
239A PHE* 4.6 4.5 - + - -
242A ILE* 3.3 32.3 - - + -
243A LEU* 5.5 0.4 - - + -
246A LEU* 3.5 38.1 - - + -
251A ILE* 4.1 2.0 - - + -
252A PRO 2.9 10.5 + - - +
253A VAL* 4.3 14.4 - - + -
254A ILE* 2.8 27.5 + - - +
276A PHE* 6.1 0.2 - + - -
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Residues in contact with PHE 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ASN* 3.3 32.1 - - - -
124A MET* 3.7 27.1 - - + -
125A VAL* 3.7 22.9 - - + -
128A LEU* 4.1 13.0 - - + -
143A ILE* 3.8 27.8 - - + -
144A LEU 3.0 13.3 + - - +
145A THR* 3.9 16.9 - - + +
146A ARG* 4.1 5.0 + - - -
151A HIS* 4.1 12.1 + - + -
160A MET* 3.4 16.2 - - + -
219A GLY 4.8 1.3 - - - -
220A PHE* 1.3 80.8 - - - +
222A ALA* 1.3 62.8 + - - +
254A ILE* 3.3 37.9 - - + +
256A ASP* 5.3 1.8 - - + -
282A ILE* 4.5 0.4 - - + -
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Residues in contact with ALA 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ARG* 3.6 24.5 - - - +
151A HIS* 4.5 1.1 - - - -
220A PHE* 3.5 23.3 - - + -
221A PHE* 1.3 75.0 - - - +
223A GLU* 1.3 61.2 + - - +
224A PRO* 3.5 2.6 - - - +
239A PHE* 3.9 19.1 - - + -
254A ILE 3.0 8.0 + - - +
255A SER* 3.5 7.3 + - - -
256A ASP* 2.9 23.7 + - - +
276A PHE* 4.9 3.6 - - + -
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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