Contacts of the strand formed by residues 177 - 182 (chain D) in PDB entry 3AP3
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 LYS 177 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69D PRO* 6.4 1.1 - - + -
70D LEU 2.8 12.9 + - - +
71D ILE* 3.7 2.2 - - - -
72D PHE* 3.0 26.4 + - - +
175D ASN 4.4 8.0 + - - +
176D SER* 1.3 76.2 - - - +
178D PHE* 1.3 69.7 - - - +
231D GLU* 3.2 31.0 + - - +
232D LYS* 3.5 15.5 - - + +
255D PHE* 3.4 31.7 + - + -
256D LEU* 4.1 36.1 + - + +
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Residues in contact with PHE 178 (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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72D PHE* 3.4 37.5 - + + +
163D LEU* 4.6 10.5 - - + -
166D SER* 3.7 24.0 - - - -
169D LEU* 3.6 31.9 - - + -
170D SER* 3.7 22.0 - - - -
176D SER* 3.5 30.5 - - - -
177D LYS* 1.3 77.0 - - - +
179D LEU* 1.3 65.8 + - - +
180D LEU 4.1 0.4 - - - -
228D VAL* 4.7 6.1 - - + -
232D LYS* 2.7 25.2 + - + +
233D CYS* 3.3 16.7 - - + -
234D LEU* 2.8 27.5 + - - -
255D PHE* 3.9 1.0 - - - -
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Residues in contact with LEU 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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71D ILE* 4.3 13.5 - - + -
72D PHE 2.9 11.7 + - - +
73D VAL* 3.7 11.2 - - + +
74D GLY 3.4 23.7 + - - +
84D MET* 4.2 18.4 - - + -
88D LEU* 3.9 28.7 - - + -
163D LEU* 3.5 5.7 - - - +
178D PHE* 1.3 72.1 - - - +
180D LEU* 1.3 61.5 - - - +
181D MET* 3.8 1.6 + - - -
234D LEU* 3.4 15.7 - - + -
236D VAL* 4.0 11.7 - - + -
252D ILE* 4.3 16.6 - - + -
255D PHE* 3.7 33.4 - - + -
256D LEU* 4.2 9.6 - - + -
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Residues in contact with LEU 180 (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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75D GLY* 4.2 10.5 - - - -
163D LEU* 3.5 26.5 - - + -
178D PHE 4.1 0.6 - - - -
179D LEU* 1.3 70.8 - - - +
181D MET* 1.3 61.4 + - - +
182D VAL* 3.4 13.4 + - + +
218D ILE* 5.4 4.9 - - + -
221D MET* 3.7 34.8 - - + +
222D TYR* 4.1 17.0 - - + -
225D CYS* 3.6 29.4 - - + -
233D CYS* 4.2 6.5 - - - -
234D LEU 2.8 14.9 + - - +
235D PRO* 3.3 6.5 - - + +
236D VAL* 2.5 31.2 + - - +
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Residues in contact with MET 181 (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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73D VAL* 4.2 8.1 - - + -
74D GLY 3.1 19.6 + - - +
75D GLY* 4.2 9.5 - - - -
76D VAL 4.7 0.9 + - - -
79D SER* 3.2 39.0 + - - +
80D GLY* 3.4 12.3 - - - +
81D THR* 3.6 28.7 - - + -
84D MET* 3.5 24.0 - - + -
179D LEU* 4.9 1.3 - - - +
180D LEU* 1.3 70.9 - - - +
182D VAL* 1.3 61.3 + - - +
183D ARG 4.0 0.2 - - - -
218D ILE* 5.6 4.2 - - - +
236D VAL* 3.3 43.7 - - + +
238D TYR* 4.3 17.5 - - + -
241D LEU* 4.3 9.0 - - + -
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Residues in contact with VAL 182 (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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180D LEU* 3.4 25.8 - - + +
181D MET* 1.3 73.2 - - - +
183D ARG* 1.3 61.1 + - - +
218D ILE* 4.9 9.9 - - + -
222D TYR* 5.5 0.7 - - + -
235D PRO* 4.3 13.2 - - + -
236D VAL 2.6 18.7 + - - +
237D TYR* 3.3 31.3 - - + -
238D TYR* 3.0 21.7 + - - +
239D GLU* 3.1 0.2 - - - +
323D LEU* 3.7 34.5 - - + -
325D TYR* 3.0 16.8 + - + +
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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