Contacts of the strand formed by residues 93 - 98 (chain A) in PDB entry 2EWC
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 ALA 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A VAL 3.0 15.1 + - - +
65A GLN* 3.1 9.3 - - + +
66A MSE 2.9 23.9 + - - -
92A PRO* 1.3 72.4 - - - +
94A ARG* 1.3 60.8 + - - +
16C THR 3.3 14.4 - - - +
19C VAL* 3.6 7.1 - - + +
26C TYR* 3.6 24.0 - - + +
27C LEU 3.7 4.9 - - - +
28C ASN* 3.5 22.9 - - - +
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Residues in contact with ARG 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A GLN* 4.3 3.8 - - - +
66A MSE 3.2 25.8 - - + +
68A CYS* 4.0 9.0 - - - -
76A ILE* 4.2 7.1 - - - +
79A MSE 3.5 27.0 - - - +
80A GLU* 3.1 22.8 + - - +
83A ILE* 3.7 16.3 - - - +
92A PRO 4.6 2.2 - - - +
93A ALA* 1.3 76.9 - - - +
95A LYS* 1.3 63.3 + - - +
96A SER* 4.2 8.4 + - - -
13C ARG* 3.0 21.6 + - - +
14C GLY 3.0 29.5 + - - -
15C HIS* 3.6 19.3 - - + +
27C LEU 5.5 0.2 - - - -
28C ASN* 2.8 23.5 + - - +
29C TYR* 3.0 39.7 + - + -
115C ASP* 4.7 1.8 - - - -
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Residues in contact with LYS 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A GLN* 4.2 1.6 - - - +
66A MSE 3.3 4.1 + - - +
67A ASP* 2.8 35.5 + - - +
68A CYS* 2.9 25.8 + - - +
94A ARG* 1.3 79.6 - - - +
96A SER* 1.3 62.9 + - - +
97A ILE* 4.0 20.1 - - + +
67B ASP* 6.0 0.2 - - - -
95B LYS* 5.7 1.1 - - - +
29C TYR* 4.3 17.7 - - + -
67C ASP* 2.7 37.4 + - + -
69C LEU* 4.1 28.3 - - + -
95C LYS* 5.7 0.9 - - - +
97C ILE* 5.1 2.5 - - - -
115C ASP* 2.8 30.0 + - - +
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Residues in contact with SER 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A CYS* 3.3 9.4 - - - +
70A PHE* 3.7 22.7 - - - -
73A VAL* 4.1 6.9 - - - +
76A ILE* 3.6 31.9 - - - +
79A MSE 4.0 8.0 - - - +
94A ARG* 4.2 6.8 + - - -
95A LYS* 1.3 77.0 + - - +
97A ILE* 1.3 66.4 + - - +
29C TYR* 5.1 4.1 - - - -
69C LEU* 3.7 14.6 - - - +
99C THR* 4.7 2.8 + - - +
100C GLU 5.2 1.0 - - - +
101C PHE* 5.4 2.8 - - - -
113C GLN* 4.9 3.4 + - - +
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Residues in contact with ILE 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ASP* 5.5 1.6 - - + -
68A CYS 2.9 9.7 + - - +
69A LEU* 3.5 16.1 - - + -
70A PHE* 2.8 27.7 + - - +
73A VAL* 4.4 4.3 - - - -
95A LYS* 4.0 22.7 - - + +
96A SER* 1.3 80.5 - - - +
98A GLN* 1.3 75.0 + - - +
99A THR* 3.9 10.5 + - - -
95B LYS* 5.2 2.7 - - - -
97B ILE* 4.2 25.4 - - + -
69C LEU* 4.1 17.7 - - + -
97C ILE* 4.0 32.5 - - + -
99C THR* 3.7 7.9 - - - +
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Residues in contact with GLN 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A PHE 3.2 5.6 - - - +
71A ARG 3.4 22.7 + - - +
72A ASP* 3.5 6.6 - - - +
73A VAL* 2.9 44.4 + - + +
74A TRP* 5.0 2.1 - - - -
97A ILE* 1.3 80.5 - - - +
99A THR* 1.3 65.7 + - - +
98B GLN 4.8 2.9 - - - +
98C GLN 4.8 2.9 - - - +
99C THR* 2.9 23.1 + - - +
100C GLU* 3.6 18.5 - - + +
100K GLU* 2.7 36.5 + - - +
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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