Contacts of the strand formed by residues 24 - 30 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19H VAL 3.8 0.3 - - - +
20H GLU* 3.7 0.2 - - - -
21H ALA* 2.8 36.6 + - - +
22H GLY 3.3 0.5 - - - +
23H ASP* 1.3 85.0 - - + +
25H TYR* 1.3 65.4 - - - +
26H TYR* 3.8 20.4 - - + -
64H VAL* 5.1 0.2 - - + -
117H VAL* 4.1 6.7 - - + -
118H ALA 3.4 11.9 - - - -
119H TYR* 3.4 26.5 - + + -
24I PHE* 3.7 22.4 - + + -
21J ALA* 3.3 33.4 - - + -
22J GLY* 5.7 0.2 - - - -
23J ASP 5.7 0.9 - - - -
24J PHE* 3.6 25.8 - + - -
26J TYR* 3.4 27.6 - + - -
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Residues in contact with TYR 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H LEU* 3.9 21.3 - - + -
19H VAL 3.2 4.5 - - - -
20H GLU* 3.5 39.6 + - + -
22H GLY 4.6 0.2 - - - -
23H ASP 3.6 21.5 - - - -
24H PHE* 1.3 74.4 - - - +
26H TYR* 1.3 64.1 + - - +
27H LEU* 4.0 1.4 + - - +
53H LEU* 5.2 0.4 - - + -
56H VAL* 3.7 31.7 + - + +
58H LEU* 3.7 27.7 - - + +
116H GLY 4.6 0.2 - - - -
117H VAL* 3.2 5.7 - - - -
118H ALA* 2.8 52.9 + - + +
120H SER* 4.1 11.1 - - - -
122H HIS* 2.9 32.5 + - - -
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Residues in contact with TYR 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H LEU* 3.3 4.6 - - - -
19H VAL* 2.8 43.9 + - + +
21H ALA* 4.4 3.6 - - + -
24H PHE* 3.8 17.2 - - + +
25H TYR* 1.3 74.7 - - - +
27H LEU* 1.3 61.9 + - - +
116H GLY 3.9 1.8 - - - -
117H VAL* 3.9 31.6 - - + -
24I PHE* 3.4 38.4 - + - -
26I TYR* 4.2 8.5 + + - -
64I VAL* 3.8 36.3 - - + +
65I GLN* 3.8 24.2 - - + -
93I ALA* 3.7 8.6 - - + +
117I VAL* 3.8 20.0 - - + +
26J TYR* 4.3 8.1 + + - -
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Residues in contact with LEU 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H GLY 3.5 2.5 - - - +
18H LEU* 3.7 24.5 - - + -
25H TYR 4.7 1.1 - - - +
26H TYR* 1.3 73.9 - - - +
28H ASN* 1.3 69.1 + - - +
30H CYS* 4.4 9.0 - - - -
49H MSE 4.0 34.5 - - + +
52H ARG* 3.8 30.3 - - + -
53H LEU* 4.2 15.7 - - + -
63H VAL* 4.9 2.0 - - + -
115H ASP* 3.5 15.8 - - - +
116H GLY 3.0 35.1 + - - +
117H VAL 4.4 2.7 - - - +
118H ALA* 4.7 8.1 - - + -
65I GLN* 5.2 4.2 + - - +
93I ALA* 3.8 4.7 - - - +
94I ARG 5.0 0.7 + - - -
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Residues in contact with ASN 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H HIS* 3.3 42.0 - - - +
16H THR 3.2 16.0 + - - +
17H GLY* 3.0 18.1 + - - +
27H LEU* 1.3 78.3 - - - +
29H TYR* 1.3 98.1 + - - +
30H CYS* 3.3 9.4 + - - -
52H ARG* 3.5 9.0 + - - +
115H ASP* 3.8 3.8 - - - +
93I ALA* 3.6 8.8 - - - +
94I ARG* 2.8 37.5 + - - +
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Residues in contact with TYR 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H ARG* 4.3 13.9 - - - -
15H HIS* 3.9 22.1 + + - -
28H ASN* 1.3 95.1 + - - +
30H CYS* 1.3 59.5 + - - +
31H VAL* 4.5 17.3 - - + -
48H GLU* 4.0 1.9 - - - +
52H ARG* 2.9 17.9 + - - -
69H LEU* 5.4 1.1 - - + -
103H HIS* 5.7 2.3 + - - -
113H GLN* 3.6 48.7 - - + +
114H VAL 3.6 6.3 - - - +
115H ASP* 3.9 6.3 - - + +
94I ARG* 3.1 36.1 + - - +
95I LYS* 4.3 16.4 - - + -
96I SER* 5.3 2.5 - - - -
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Residues in contact with CYS 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H LEU* 4.4 9.0 - - - -
28H ASN 3.5 8.3 - - - -
29H TYR* 1.3 72.3 - - - +
31H VAL* 1.3 62.7 + - - +
45H ALA* 3.4 23.9 - - - +
48H GLU* 3.5 9.2 - - + -
49H MSE 3.7 33.0 - - - -
52H ARG* 3.4 21.8 - - - -
113H GLN* 3.3 8.5 - - - -
114H VAL* 2.8 38.0 + - + +
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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