Contacts of the strand formed by residues 91 - 103 (chain D) in PDB entry 2EWY
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 SER 91 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222B GLY 4.7 3.1 + - - -
223B GLY* 4.5 14.6 + - - -
84D THR* 5.2 3.4 - - - -
85D VAL 3.2 17.5 - - - -
86D LYS* 3.9 14.4 - - - -
87D TYR* 4.6 4.5 - - - -
90D GLY* 1.3 76.5 - - - -
92D TRP* 1.3 67.0 + - - +
120D GLU* 4.9 3.2 + - - -
121D SER* 3.2 3.6 - - - -
122D GLU* 2.9 42.4 + - - +
124D PHE* 3.9 5.0 - - - +
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Residues in contact with TRP 92 (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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53D ASN* 4.1 13.0 - - + -
55D ALA* 3.6 15.0 - - + -
83D VAL* 3.6 30.3 - - + -
84D THR* 3.1 17.4 + - - -
85D VAL* 3.2 44.2 + - + -
87D TYR* 2.8 33.2 + + - -
91D SER* 1.3 76.8 - - - +
93D THR* 1.3 74.4 + - - +
94D GLY 3.9 2.0 - - - -
116D ALA* 3.7 24.7 - - + -
118D ILE* 3.5 30.1 - - + -
120D GLU* 3.1 13.2 - - - +
121D SER* 4.0 4.0 - - - -
124D PHE* 3.4 35.6 - + - -
134D ILE* 4.3 1.6 - - + +
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Residues in contact with THR 93 (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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310B ARG* 2.8 33.0 + - - +
386B PHE* 3.7 24.9 - - + -
83D VAL 3.3 15.5 - - - +
84D THR* 3.5 7.8 + - - -
92D TRP* 1.3 82.7 + - - +
94D GLY* 1.3 59.7 + - - +
118D ILE* 3.4 1.4 - - - -
119D PHE* 2.8 41.9 + - + -
120D GLU* 2.6 26.6 + - - -
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Residues in contact with GLY 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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82D ASP* 3.2 3.3 - - - +
83D VAL* 2.8 37.7 + - - +
92D TRP* 3.9 6.6 - - - -
93D THR* 1.3 76.9 - - - +
95D PHE* 1.3 63.6 + - - -
117D THR 2.8 20.4 - - - -
118D ILE* 4.0 0.2 - - - -
119D PHE* 3.4 11.2 - - - -
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Residues in contact with PHE 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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384B GLY 5.5 2.2 - - - -
76D TYR* 4.4 11.3 + - - +
78D SER* 5.7 3.6 - - - +
81D PHE 4.5 1.1 - - - +
82D ASP* 3.2 26.2 - - - +
94D GLY* 1.3 72.6 - - - -
96D VAL* 1.3 63.6 + - - +
115D ILE 3.3 5.2 - - - +
116D ALA* 3.4 0.9 - - - -
117D THR* 2.9 45.6 + - + -
119D PHE* 3.2 38.8 - + + -
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Residues in contact with VAL 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D TYR* 3.9 4.1 + - - -
78D SER* 4.3 1.9 + - - -
79D LYS* 3.0 34.3 + - + +
80D GLY 4.0 1.7 + - - -
81D PHE* 2.8 47.3 + - + +
83D VAL* 3.6 34.1 - - + +
95D PHE* 1.3 73.9 - - - +
97D GLY* 1.3 63.1 + - - +
114D ASN* 5.2 1.6 - - + -
115D ILE 3.6 5.6 - - - +
116D ALA* 5.2 2.9 - - + -
149D LEU* 3.7 34.1 - - + -
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Residues in contact with GLY 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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76D TYR* 3.5 12.5 + - - -
77D ARG 3.4 13.0 - - - -
79D LYS* 3.8 9.3 - - - +
95D PHE 3.7 0.2 + - - -
96D VAL* 1.3 75.9 - - - +
98D GLU* 1.3 62.3 + - - +
114D ASN* 3.2 7.4 - - - +
115D ILE* 2.7 42.5 + - - -
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Residues in contact with GLU 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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75D THR 4.6 0.7 - - - -
76D TYR* 3.2 5.9 - - - -
77D ARG* 3.0 49.3 + - + +
79D LYS* 3.9 29.6 - - + -
97D GLY* 1.3 77.6 - - - +
99D ASP* 1.3 67.2 + - - +
112D LEU* 3.8 30.8 - - + +
113D VAL 3.4 9.2 - - - +
114D ASN* 4.2 5.6 - - - +
115D ILE* 4.1 2.9 - - - -
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Residues in contact with ASP 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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36D ILE* 4.6 9.6 - - + -
37D GLY* 3.2 14.2 - - - -
68D PHE* 3.7 6.3 - - + -
73D SER* 2.7 24.1 + - - -
75D THR* 2.6 26.0 + - - -
76D TYR* 3.1 25.0 - - + +
98D GLU* 1.3 78.8 - - - +
100D LEU* 1.3 78.8 + - - +
101D VAL* 4.6 1.1 - - + -
111D PHE 3.7 0.3 - - - +
112D LEU* 3.5 10.2 - - - +
113D VAL* 3.1 34.2 + - + +
115D ILE* 4.4 7.1 - - + +
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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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35D LEU 4.0 0.3 - - - +
36D ILE* 3.8 1.6 - - - +
37D GLY* 3.0 29.1 + - - +
38D THR* 4.5 6.1 - - - +
75D THR* 3.8 28.7 - - + +
99D ASP* 1.3 86.9 + - - +
101D VAL* 1.3 62.9 + - - +
110D SER* 4.2 22.2 - - - +
111D PHE* 3.4 19.7 - - - +
112D LEU* 3.6 24.2 - - + +
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Residues in contact with VAL 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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34D MET* 4.0 30.7 - - + -
35D LEU 3.5 9.6 - - - +
36D ILE* 4.7 9.6 - - + -
54D PHE* 4.1 10.5 - - + -
99D ASP* 4.0 2.2 - - + +
100D LEU* 1.3 79.2 - - - +
102D THR* 1.3 69.6 + - - +
103D ILE* 4.7 0.7 - - + -
110D SER* 3.0 5.2 - - - -
111D PHE* 2.9 45.3 + - + +
113D VAL* 3.2 34.3 - - + -
115D ILE* 5.9 0.4 - - + -
152D PHE* 4.1 11.7 - - + -
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Residues in contact with THR 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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34D MET* 3.6 2.1 - - - -
35D LEU* 2.9 54.3 + - + -
40D PRO* 6.5 0.4 - - - -
101D VAL* 1.3 74.2 - - - +
103D ILE* 1.3 63.8 + - - +
104D PRO* 3.1 13.4 - - + +
107D PHE 3.9 11.9 - - - +
108D ASN* 4.4 15.2 + - + +
110D SER* 3.3 26.7 + - - +
111D PHE* 5.0 0.9 - - - -
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Residues in contact with ILE 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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21D ASN* 5.6 0.4 - - - +
32D LEU* 4.0 32.3 - - + -
33D GLU 4.4 2.7 - - - +
34D MET* 4.0 21.1 - - + -
101D VAL* 4.7 0.4 - - + -
102D THR* 1.3 75.7 - - - +
104D PRO* 1.3 68.8 - - + +
105D LYS 3.2 17.7 + - - +
107D PHE* 2.7 46.5 + - + +
111D PHE* 4.2 15.4 - - + -
152D PHE* 4.2 14.8 - - + -
156D LEU* 4.7 0.2 - - + -
189D LEU* 3.5 30.5 - - + -
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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