Contacts of the helix formed by residues 93 - 105 (chain D) in PDB entry 3ERE
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 93 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91D SER 3.3 0.6 - - - -
92D GLY* 1.3 76.7 - - - +
94D THR* 1.3 63.6 + - - +
96D ARG* 3.6 1.2 + - - +
97D MET* 3.1 25.3 + - - +
130D ALA 4.5 1.7 - - - +
133D ARG* 3.7 22.0 + - - +
134D ALA* 3.5 9.3 - - - +
172D SO4 3.0 27.6 + - - -
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Residues in contact with THR 94 (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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91D SER* 3.1 24.8 + - - -
92D GLY 3.3 2.6 + - - -
93D GLY* 1.3 77.8 - - - +
95D ASP* 1.3 63.4 + - - +
97D MET* 3.7 12.9 - - + +
98D ALA* 3.0 28.4 + - + +
134D ALA* 3.9 14.8 + - - +
136D LEU* 4.9 7.3 - - + +
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Residues in contact with ASP 95 (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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90D VAL* 5.8 0.9 - - - +
91D SER* 2.8 33.2 + - - +
94D THR* 1.3 79.5 - - - +
96D ARG* 1.3 61.7 + - - +
98D ALA* 3.1 8.1 + - - +
99D ARG* 2.8 47.3 + - - +
172D SO4 3.4 7.3 + - - +
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Residues in contact with ARG 96 (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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29D LEU 3.5 12.3 + - - -
30D SER 3.2 22.1 + - - +
31D SER* 3.4 4.6 - - - +
32D ALA 2.8 43.4 + - - +
33D GLN* 4.2 5.9 - - - +
77D ILE* 4.5 6.1 - - - +
78D TYR 5.4 0.2 + - - -
79D VAL* 5.0 6.5 - - - +
93D GLY 4.2 0.4 - - - +
95D ASP* 1.3 71.6 - - - +
97D MET* 1.3 61.4 + - - +
99D ARG* 3.3 31.4 + - - +
100D LEU* 3.0 58.8 + - + +
130D ALA* 5.1 4.9 - - + -
133D ARG* 4.1 20.2 - - - +
172D SO4 2.8 22.4 + - - +
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Residues in contact with MET 97 (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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93D GLY 3.1 18.4 + - - +
94D THR* 4.1 17.3 - - + +
96D ARG* 1.3 78.5 - - - +
98D ALA* 1.3 58.2 + - + +
100D LEU* 3.1 3.5 + - - +
101D LEU* 2.8 50.8 + - + +
127D LEU* 4.5 0.6 - - + +
130D ALA* 3.9 20.6 - - + +
131D ILE* 4.0 30.7 - - + +
134D ALA* 3.9 12.1 - - + -
136D LEU* 3.8 38.4 - - + -
165D MET* 5.4 0.9 - - - -
166D PHE* 4.5 2.9 - - + -
169D LEU* 4.3 13.9 - - + -
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Residues in contact with ALA 98 (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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94D THR* 3.0 20.9 + - + +
95D ASP* 3.5 10.3 - - - +
97D MET* 1.3 78.1 - - + +
99D ARG* 1.3 62.3 + - - +
101D LEU* 3.4 12.5 + - - +
102D GLY* 3.1 19.1 + - - -
169D LEU* 4.4 23.3 - - + +
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Residues in contact with ARG 99 (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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31D SER* 3.3 37.1 + - - -
32D ALA* 5.3 0.8 - - - +
33D GLN* 3.4 33.8 + - + +
95D ASP* 2.8 32.1 + - - +
96D ARG* 3.4 42.0 - - - +
98D ALA* 1.3 77.8 - - + +
100D LEU* 1.3 63.3 + - + +
102D GLY* 3.4 2.6 + - - -
103D GLU* 3.2 22.2 + - - +
172D SO4 4.7 3.2 + - - -
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Residues in contact with LEU 100 (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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33D GLN* 5.6 2.0 - - + -
77D ILE* 3.8 30.1 - - + -
79D VAL* 5.6 2.5 - - + -
96D ARG* 3.0 47.3 + - + +
97D MET 3.7 3.8 - - - +
99D ARG* 1.3 75.0 - - - +
101D LEU* 1.3 56.5 + - - +
103D GLU* 3.6 3.3 - - + -
104D LEU* 2.7 54.0 + - + +
126D TYR* 4.2 16.6 - - + +
127D LEU* 3.9 13.6 - - + +
130D ALA* 3.6 26.0 - - + -
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Residues in contact with LEU 101 (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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97D MET* 2.8 30.9 + - + +
98D ALA* 3.5 7.0 - - - +
100D LEU* 1.3 77.2 - - - +
102D GLY* 1.3 59.1 + - - +
105D LEU* 2.9 53.4 + - + +
117D LEU* 5.0 0.4 - - + -
127D LEU* 3.5 33.4 - - + -
131D ILE* 4.6 5.2 - - + -
166D PHE* 3.9 26.5 - - + -
169D LEU* 3.7 44.9 - - + +
170D ARG* 4.4 1.7 - - - -
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Residues in contact with GLY 102 (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 ALA* 4.8 5.5 - - - +
98D ALA 3.1 10.0 + - - -
99D ARG 3.8 3.4 - - - -
101D LEU* 1.3 80.7 - - - +
103D GLU* 1.3 59.2 + - - +
105D LEU 5.3 0.5 - - - +
169D LEU 3.8 7.1 + - - -
170D ARG* 3.9 19.7 - - - +
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Residues in contact with GLU 103 (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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33D GLN* 3.6 14.8 - - - +
35D ARG* 2.9 30.7 + - - -
69D ARG 4.4 0.9 - - - +
70D GLY* 3.5 22.3 - - - -
71D ALA* 2.8 26.2 + - - +
75D THR 4.1 0.2 - - - +
76D GLY* 3.5 19.6 - - - -
77D ILE* 3.8 18.7 + - + +
99D ARG 3.2 15.8 + - - +
100D LEU* 3.8 6.1 - - + +
101D LEU 3.1 0.6 - - - -
102D GLY* 1.3 79.5 - - - +
104D LEU* 1.3 69.2 - - + +
105D LEU 3.9 0.2 - - - -
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Residues in contact with LEU 104 (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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68D LEU* 4.1 26.2 - - + -
69D ARG 3.6 23.8 - - - +
71D ALA* 3.6 5.3 - - - +
77D ILE* 5.3 1.6 - - + -
100D LEU* 2.7 39.0 + - + +
103D GLU* 1.3 91.0 - - + +
105D LEU* 1.3 61.9 + - - +
106D VAL 3.2 3.6 + - - -
119D THR* 3.2 27.4 - - + -
120D PRO* 3.2 7.5 - - + +
123D ALA* 3.9 30.1 - - + +
126D TYR* 4.7 1.8 - - + -
127D LEU* 4.3 17.0 - - + +
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Residues in contact with LEU 105 (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 ALA* 3.4 10.6 - - - +
100D LEU 4.1 0.2 + - - -
101D LEU* 2.9 38.1 + - + +
102D GLY 5.3 0.3 - - - +
104D LEU* 1.3 70.1 - - - +
106D VAL* 1.3 56.5 + - - +
107D SER 3.4 23.6 - - - +
108D THR* 3.8 14.6 - - + -
117D LEU* 3.7 28.7 - - + -
118D ARG 3.7 5.2 - - - +
127D LEU* 4.5 7.3 - - + +
166D PHE* 3.3 31.9 - - + +
170D ARG* 3.3 41.2 + - + +
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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