Contacts of the strand formed by residues 24 - 30 (chain I) 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 PHE 24 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H ALA* 3.3 27.4 - - + -
22H GLY* 5.8 0.2 - - - -
23H ASP 5.6 0.7 - - - -
24H PHE* 3.7 29.4 - + + -
26H TYR* 3.4 35.2 - + - -
19I VAL 3.7 0.3 - - - +
20I GLU* 3.6 0.5 - - - +
21I ALA* 2.8 37.7 + - - +
23I ASP* 1.3 85.2 - - + +
25I TYR* 1.3 66.9 + - - +
26I TYR* 3.7 21.0 - - + -
64I VAL* 4.9 0.4 - - + -
117I VAL* 4.0 6.7 - - + -
118I ALA 3.4 11.2 - - - -
119I TYR* 3.4 26.5 - + + -
24J PHE* 3.8 20.6 - + + -
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Residues in contact with TYR 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I LEU* 3.9 21.3 - - + -
19I VAL 3.3 3.8 - - - -
20I GLU* 3.5 43.3 + - + -
23I ASP 3.5 20.4 - - - -
24I PHE* 1.3 74.3 - - - +
26I TYR* 1.3 62.1 + - - +
27I LEU* 4.0 1.8 + - - +
53I LEU* 5.0 0.2 - - + -
56I VAL* 3.8 29.3 + - + +
58I LEU* 3.7 26.0 - - + +
116I GLY 4.0 0.2 - - - +
117I VAL* 3.3 5.7 - - - +
118I ALA* 2.8 56.1 + - + +
120I SER* 4.0 11.6 + - - -
122I HIS* 3.2 28.7 + + - -
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Residues in contact with TYR 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H TYR* 4.2 11.3 + + - -
18I LEU* 3.4 4.4 - - - -
19I VAL* 2.8 45.9 + - + +
21I ALA* 4.6 2.5 - - + -
24I PHE* 3.7 27.1 - - + +
25I TYR* 1.3 74.9 - - - +
27I LEU* 1.3 61.8 + - - +
116I GLY 3.8 2.9 - - - +
117I VAL* 3.8 29.2 - - + -
24J PHE* 3.3 33.0 - + - -
26J TYR* 4.3 5.1 + + - -
64J VAL* 3.8 36.1 - - + +
65J GLN* 3.8 24.7 - - + -
93J ALA* 3.6 6.4 - - + +
117J VAL* 3.9 19.9 - - + +
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Residues in contact with LEU 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I GLY 3.4 2.2 - - - +
18I LEU* 3.8 15.7 - - + -
25I TYR 4.9 4.0 - - - +
26I TYR* 1.3 73.2 - - - +
28I ASN* 1.3 69.4 + - - +
30I CYS* 4.4 9.9 - - - -
49I MSE 4.1 33.0 - - + +
52I ARG* 3.5 38.8 - - + -
53I LEU* 4.3 18.2 - - + -
63I VAL* 5.1 2.2 - - + -
115I ASP* 3.4 15.6 - - - +
116I GLY 3.0 32.8 + - - +
117I VAL 4.6 1.1 - - - +
118I ALA* 5.0 4.5 - - + -
65J GLN* 5.2 3.8 + - - +
93J ALA* 3.7 5.7 - - - +
94J ARG 5.0 0.7 + - - +
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Residues in contact with ASN 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15I HIS* 3.3 41.6 - - - +
16I THR 3.3 14.1 - - - +
17I GLY* 2.9 18.1 + - - +
27I LEU* 1.3 79.1 - - - +
29I TYR* 1.3 101.2 + - - +
30I CYS* 3.3 9.9 + - - -
52I ARG* 3.4 8.9 + - - +
115I ASP* 3.9 2.4 - - - +
93J ALA* 3.5 9.7 - - - +
94J ARG* 2.8 36.5 + - - +
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Residues in contact with TYR 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13I ARG* 4.9 10.7 + - - +
15I HIS* 3.9 23.0 + + - -
28I ASN* 1.3 98.3 - - - +
30I CYS* 1.3 63.2 + - - +
31I VAL* 4.7 13.9 - - + -
48I GLU* 4.2 1.5 - - - +
52I ARG* 2.9 17.2 + - - -
69I LEU* 5.6 0.7 - - + -
113I GLN* 3.8 45.3 - - + +
114I VAL 3.5 8.3 - - - +
115I ASP* 3.8 7.0 - - + +
80J GLU* 5.7 0.5 + - - -
94J ARG* 3.0 36.3 + - - +
95J LYS* 4.2 17.7 - - + -
96J SER 5.4 1.1 - - - -
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Residues in contact with CYS 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I LEU* 4.4 8.1 - - - -
28I ASN 3.5 9.0 - - - -
29I TYR* 1.3 73.2 - - - +
31I VAL* 1.3 62.3 + - - +
45I ALA* 3.5 23.0 - - - +
48I GLU* 3.7 8.7 - - + -
49I MSE 3.7 33.9 - - - -
52I ARG* 3.4 21.1 - - - -
113I GLN* 3.3 8.5 - - - -
114I VAL* 2.6 39.5 + - + +
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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