Contacts of the strand formed by residues 174 - 179 (chain D) in PDB entry 3N2N
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 174 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D TYR* 5.4 7.9 - - + +
142D ALA* 5.8 5.4 - - + -
143D SER 2.8 15.7 + - - +
144D VAL* 3.5 14.4 - - + +
145D ILE 2.8 27.7 + - - +
172D GLY 4.7 4.9 - - - +
173D ALA* 1.3 76.1 - - - +
175D VAL* 1.3 62.0 + - - +
176D TYR* 3.7 27.5 + - + +
193D ASP* 3.6 17.5 - - - +
197D HIS* 3.7 14.1 - - + +
215D ILE* 6.2 2.2 - - + -
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Residues in contact with VAL 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D PHE* 3.7 36.3 - - + -
145D ILE* 3.7 18.4 - - + -
165D ALA 4.3 10.3 - - - +
168D SER* 4.5 2.5 - - - -
169D ARG* 3.6 24.0 - - + +
173D ALA* 4.6 1.3 - - + -
174D ILE* 1.3 75.8 - - - +
176D TYR* 1.3 72.6 + - - +
191D ILE* 3.6 17.7 - - + +
192D ALA* 3.4 5.5 - - - +
193D ASP* 2.8 40.9 + - - +
197D HIS* 3.4 8.3 - - - +
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Residues in contact with TYR 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D VAL* 3.6 28.9 - - + -
145D ILE 2.7 12.4 + - - +
146D ILE* 4.4 12.8 - - + -
147D ALA* 2.9 24.9 + - - +
174D ILE* 3.7 20.3 - - + +
175D VAL* 1.3 83.1 - - - +
177D ALA* 1.3 62.0 + - - +
178D VAL* 5.4 0.4 - - + -
196D ASP 4.8 0.9 - - - -
197D HIS* 3.3 43.8 + + - +
199D PHE* 3.8 16.4 - + - -
208D LEU* 4.1 15.9 - - + -
211D ILE* 3.6 46.5 - - + +
215D ILE* 5.9 0.2 - - + -
195F LYS* 5.5 0.9 + - - -
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Residues in contact with ALA 177 (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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147D ALA* 3.3 12.8 - - + +
149D THR* 5.6 1.8 - - + -
176D TYR* 1.3 72.8 - - - +
178D VAL* 1.3 63.8 + - - +
179D GLY 4.0 0.2 - - - -
188D LEU* 4.1 31.6 - - + +
191D ILE* 5.1 4.9 - - + -
192D ALA* 3.8 19.6 - - + +
197D HIS 2.9 7.8 + - - +
198D VAL* 3.3 7.4 - - + +
199D PHE 3.0 23.7 + - - +
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Residues in contact with VAL 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D PHE* 3.9 19.5 - - + -
146D ILE* 3.8 22.9 - - + -
147D ALA 2.8 9.5 + - - +
148D LEU* 3.4 30.7 - - + +
149D THR 3.2 24.1 + - - +
176D TYR* 5.4 0.2 - - + -
177D ALA* 1.3 76.6 - - - +
179D GLY* 1.3 61.9 + - - +
180D VAL 3.9 0.3 + - - -
188D LEU* 4.6 2.0 - - - +
199D PHE* 3.2 12.1 - - + +
200D PRO 4.1 2.9 - - - +
201D VAL* 3.6 27.4 - - + -
204D GLY* 5.0 0.9 - - - -
208D LEU* 4.2 15.9 - - + -
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Residues in contact with GLY 179 (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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149D THR 3.4 7.0 - - - -
177D ALA 4.0 1.6 + - - -
178D VAL* 1.3 71.8 - - - +
180D VAL* 1.3 62.5 + - - -
181D LYS 4.8 0.3 - - - +
183D PHE* 3.5 32.0 - - - -
188D LEU* 3.8 7.9 - - - +
199D PHE 2.7 14.6 + - - -
201D VAL* 2.9 29.2 + - - +
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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