Contacts of the strand formed by residues 165 - 170 (chain D) in PDB entry 3NY5
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 GLN 165 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C MSE 4.2 4.0 - - - +
153C GLN* 3.7 32.9 + - - +
155C PRO* 3.8 34.2 - - + +
173C CYS* 5.5 0.4 - - - -
218C THR* 3.8 5.2 - - + +
160D PHE* 3.6 4.5 - - - +
161D LEU* 2.6 36.4 + - + +
162D PRO 3.6 11.9 - - - +
163D ASN* 3.1 19.1 + - - +
164D LYS* 1.3 79.1 - - - +
166D ARG* 1.3 62.4 + - - +
188D ARG* 2.8 46.1 + - - +
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Residues in contact with ARG 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B THR 4.7 0.4 + - - -
234B THR* 2.9 32.9 + - - -
235B HIS 4.6 6.1 + - - -
173C CYS* 3.6 23.8 - - - +
174C GLY* 4.3 0.8 - - - +
213C ASP* 2.9 28.5 + - - -
215C SER* 2.9 43.1 + - - +
216C TRP* 3.6 39.9 - - + +
218C THR* 4.3 3.9 + - - +
159D VAL 3.3 12.8 - - - +
160D PHE* 3.9 21.5 - - + -
161D LEU* 4.0 4.7 - - - +
164D LYS 4.6 1.1 + - - +
165D GLN* 1.3 82.9 - - - +
167D THR* 1.3 66.3 + - - +
188D ARG* 4.0 12.0 + - - +
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Residues in contact with THR 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C TRP* 3.5 19.6 + - - -
218C THR 5.2 5.4 + - - -
220C GLU* 6.0 2.3 - - - +
159D VAL* 2.8 52.2 + - + +
161D LEU* 3.7 22.0 - - + -
166D ARG* 1.3 76.5 - - - +
168D VAL* 1.3 72.3 + - - +
169D VAL* 4.4 4.6 - - + +
181D LEU* 4.0 15.5 - - + -
184D ALA* 4.0 14.2 - - + +
187D MSE 6.1 0.6 - - - +
188D ARG* 5.4 1.3 - - - -
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Residues in contact with VAL 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C ARG* 4.8 21.1 + - - +
216C TRP* 3.7 43.4 + - + +
217C LEU* 6.3 1.8 - - + -
156D ILE* 3.5 46.9 - - + -
157D VAL 3.4 6.3 - - - +
158D ARG* 4.6 3.8 - - + -
167D THR* 1.3 82.6 + - - +
169D VAL* 1.3 66.6 + - - +
170D PRO* 4.6 1.7 - - - +
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Residues in contact with VAL 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D ILE* 3.2 3.5 - - - +
157D VAL* 2.9 41.9 + - + +
159D VAL* 4.3 7.9 - - + -
167D THR* 4.4 5.6 - - + +
168D VAL* 1.3 83.3 - - - +
170D PRO* 1.3 75.9 - - + +
180D SER* 3.5 30.3 - - - +
181D LEU* 3.7 22.4 - - + -
214D ILE* 3.6 31.0 - - + -
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Residues in contact with PRO 170 (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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201C GLN* 4.6 20.6 - - - +
155D PRO 3.6 8.1 - - - +
156D ILE* 4.3 6.3 - - + -
168D VAL 4.6 1.1 - - - +
169D VAL* 1.3 99.3 - - + +
171D ALA* 1.3 60.0 + - - +
172D ARG* 3.4 27.5 + - + +
180D SER* 4.5 4.6 + - - +
214D ILE* 4.1 6.6 - - - +
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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