Contacts of the helix formed by residues 80 - 91 (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 GLY 80 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D A3P 2.7 34.3 + - - -
78D ARG 3.2 3.0 + - - -
79D SER* 1.3 71.3 - - - +
81D THR* 1.3 60.7 + - - +
82D THR 3.4 2.0 - - - -
83D LEU* 3.8 8.8 + - - +
84D MET 3.2 15.6 + - - -
181D MET* 3.4 13.3 - - - +
238D TYR* 3.8 19.2 - - - -
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Residues in contact with THR 81 (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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1D A3P 2.5 29.5 + - - +
73D VAL* 3.8 1.5 - - - +
74D GLY* 3.4 32.5 - - - +
75D GLY 4.0 10.3 - - - +
76D VAL 4.2 5.4 - - - +
79D SER 4.0 1.8 - - - +
80D GLY* 1.3 72.4 - - - +
82D THR* 1.3 60.4 + - - +
84D MET* 3.4 2.8 + - - +
85D ARG* 3.0 29.8 + - - +
158D LYS* 3.4 32.4 + - - +
160D PRO* 4.3 7.9 - - + +
181D MET* 3.6 18.6 - - + -
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Residues in contact with THR 82 (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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1D A3P 2.7 29.0 + - - -
81D THR* 1.3 69.0 + - - +
83D LEU* 1.3 54.5 + - - -
85D ARG* 3.1 28.0 - - - +
86D ALA* 2.6 37.6 + - - +
158D LYS* 3.3 19.8 + - - +
279D LEU* 4.7 2.2 - - + -
283D GLU* 4.4 11.1 + - + +
285D SER* 3.3 22.9 - - - +
289D VAL* 3.8 23.3 - - + -
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Residues in contact with LEU 83 (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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1D A3P 3.5 60.9 + - + +
80D GLY 3.8 9.3 + - - +
81D THR 3.4 0.2 - - - -
82D THR* 1.3 75.1 - - - +
84D MET* 1.3 63.5 + - - +
86D ALA* 3.0 4.0 + - + +
87D MET* 2.9 37.6 + - + +
238D TYR* 4.2 8.5 - - + -
241D LEU* 4.5 12.6 - - + -
242D VAL* 4.2 19.5 - - + -
267D HIS* 4.2 18.8 - - + +
289D VAL* 3.7 9.1 - - + +
293D VAL* 4.5 13.5 - - + -
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Residues in contact with MET 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D VAL* 3.7 15.0 - - + -
80D GLY 3.2 5.2 + - - +
81D THR 3.5 8.5 - - - +
82D THR 3.2 0.2 - - - -
83D LEU* 1.3 81.3 - - - +
85D ARG* 1.3 62.6 + - - +
87D MET* 3.2 11.3 + - + +
88D LEU* 3.2 41.5 + - + +
179D LEU* 4.2 12.1 - - + -
181D MET* 3.5 35.4 - - + +
236D VAL* 4.3 6.3 - - - -
241D LEU* 4.5 7.4 - - - -
249D LEU* 3.8 10.3 - - + -
252D ILE* 3.7 31.6 - - + -
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Residues in contact with ARG 85 (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* 4.4 3.1 - - + +
81D THR 3.0 13.1 + - - +
82D THR* 3.1 28.5 + - - +
84D MET* 1.3 79.5 - - - +
86D ALA* 1.3 58.9 + - - +
88D LEU* 2.7 33.1 + - - +
89D ASP* 2.9 30.4 + - - +
96D CYS* 3.7 22.0 - - + -
97D GLY 3.1 23.5 + - - -
98D GLU* 3.7 18.0 - - - +
158D LYS* 3.8 24.5 - - + +
277D VAL* 3.9 9.2 - - - +
278D SER 2.7 30.9 + - - -
279D LEU* 3.1 23.2 - - - +
283D GLU* 4.1 5.7 + - - -
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Residues in contact with ALA 86 (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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82D THR 2.6 23.0 + - - +
83D LEU* 3.0 6.7 + - - +
85D ARG* 1.3 81.9 - - - +
87D MET* 1.3 61.3 + - - +
89D ASP* 3.4 3.7 + - - -
90D ALA 3.6 1.6 + - - -
267D HIS* 4.1 12.8 - - - +
277D VAL* 3.2 41.2 - - + +
279D LEU* 5.0 0.4 - - + -
289D VAL* 3.8 27.1 - - + -
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Residues in contact with MET 87 (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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83D LEU* 2.9 26.5 + - + +
84D MET* 3.6 16.8 - - + +
85D ARG 3.1 0.2 - - - -
86D ALA* 1.3 76.3 - - - +
88D LEU* 1.3 61.9 + - - +
89D ASP 3.4 0.2 - - - -
90D ALA* 4.0 8.9 + - - +
91D HIS* 4.0 6.4 + - - +
241D LEU* 3.5 39.5 - - + -
245D PRO* 5.4 2.0 - - - -
249D LEU* 3.6 26.0 - - + -
264D VAL* 3.6 39.1 - - + +
265D LEU* 5.4 1.1 - - - -
267D HIS* 4.1 20.2 - - + -
293D VAL* 4.0 22.9 - - - -
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Residues in contact with LEU 88 (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* 4.5 9.2 - - + -
73D VAL* 3.7 28.7 - - + -
84D MET* 3.3 38.6 - - + +
85D ARG* 2.7 16.3 + - - +
87D MET* 1.3 73.4 - - - +
89D ASP* 1.3 59.6 + - - -
91D HIS* 3.4 10.2 - - + +
94D VAL* 3.2 33.9 - - + +
96D CYS* 3.9 13.7 - - - -
179D LEU* 3.9 8.1 - - + -
249D LEU* 4.5 7.9 - - + -
252D ILE* 4.4 6.1 - - + -
253D LEU* 4.5 9.0 - - + -
256D LEU* 4.4 22.4 - - + -
264D VAL* 6.3 0.2 - - + -
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Residues in contact with ASP 89 (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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85D ARG* 2.9 20.5 + - - +
86D ALA 3.7 7.4 - - - +
88D LEU* 1.3 75.5 - - - +
90D ALA* 1.3 55.8 + - - +
91D HIS 2.9 7.2 - - - +
94D VAL 3.0 6.5 - - - +
95D ARG* 3.3 25.7 - - - +
96D CYS* 3.4 6.6 + - - +
97D GLY* 2.6 30.8 + - - -
275D GLY 2.6 29.3 - - - +
276D GLY 2.7 25.7 - - - +
277D VAL* 3.5 17.5 - - + -
278D SER* 4.1 4.3 + - - -
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Residues in contact with ALA 90 (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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86D ALA 3.6 3.5 + - - +
87D MET 4.1 9.2 - - - +
88D LEU 3.4 0.2 - - - -
89D ASP* 1.3 73.1 - - - +
91D HIS* 1.3 65.5 + - - +
92D PRO* 3.3 6.6 - - - +
263D ALA* 4.0 20.4 - - - +
264D VAL* 5.0 0.2 - - - -
267D HIS* 4.1 10.8 - - + -
270D LEU* 3.2 38.7 - - + +
275D GLY 4.4 2.3 - - - +
276D GLY* 3.9 8.4 - - - -
277D VAL* 3.7 12.5 - - + +
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Residues in contact with HIS 91 (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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87D MET 4.0 5.3 + - - +
88D LEU* 3.4 18.2 + - - +
89D ASP 2.9 5.6 - - - +
90D ALA* 1.3 76.5 - - - +
92D PRO* 1.3 76.1 - - + +
93D GLU* 3.0 60.8 + - + +
94D VAL* 2.9 34.2 + - + +
253D LEU* 4.2 17.5 - - + -
258D ILE* 3.3 24.0 - - + +
259D ALA 3.3 10.6 + - - -
260D TRP 5.5 0.4 - - - -
261D SER* 3.6 26.1 - - - -
263D ALA* 5.2 0.4 - - - +
264D VAL* 4.7 8.4 - - + +
275D GLY 3.4 0.9 - - - +
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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