Contacts of the strand formed by residues 109 - 116 (chain E) in PDB entry 5EHD
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 VAL 109 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E CYS 4.0 0.3 - - - +
22E GLU* 3.4 2.6 - - - -
23E LEU* 2.8 39.0 + - + +
47E VAL* 3.5 31.9 - - + -
48E SER 3.7 6.7 - - - +
49E LEU* 3.7 19.3 - - + -
58E HIS* 3.8 14.4 - - + -
60E VAL* 3.6 11.7 - - + -
79E LEU* 4.2 3.4 - - + -
102E LEU* 3.5 28.0 - - + -
107E GLY* 4.1 0.7 - - - -
108E PRO* 1.3 80.3 - - - +
110E HIS* 1.3 66.9 + - - +
111E ILE* 4.1 2.6 + - + -
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Residues in contact with HIS 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D ILE* 5.3 2.5 - - + -
75D THR* 3.3 41.8 + - + +
103D LYS* 3.5 26.0 + - - -
21E CYS 3.6 5.8 - - - +
22E GLU* 3.6 35.8 + - + -
46E THR 3.8 0.3 - - - +
47E VAL* 3.3 5.7 - - - +
48E SER* 2.8 39.4 + - - +
49E LEU 4.3 0.2 - - - -
50E GLY* 3.5 33.9 + - - -
51E ALA 5.0 0.7 - - - -
108E PRO* 4.6 6.7 - - + -
109E VAL* 1.3 73.4 - - - +
111E ILE* 1.3 63.3 + - - +
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Residues in contact with ILE 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D VAL* 4.8 2.3 - - - +
75D THR 4.9 2.5 + - - -
19E PHE* 4.3 8.7 - - + -
20E GLY* 3.2 4.4 - - - -
21E CYS* 3.0 40.1 + - - +
23E LEU* 3.7 30.5 - - + -
44E LEU* 4.0 24.9 - - + -
46E THR 3.3 8.1 - - - +
47E VAL* 4.3 16.8 - - + -
60E VAL* 3.8 18.2 - - + -
76E LEU* 5.5 2.9 - - + -
89E LEU* 6.1 0.4 - - + -
100E LEU* 3.9 20.0 - - + -
109E VAL* 4.7 1.8 - - + +
110E HIS* 1.3 81.4 - - - +
112E SER* 1.3 69.5 + - - +
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Residues in contact with SER 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D VAL* 3.9 19.7 - - - -
75D THR 3.3 20.4 + - - -
76D LEU* 4.4 1.1 - - - +
92D PHE* 3.4 17.1 - - - -
19E PHE* 3.4 8.1 - - - -
44E LEU* 3.9 1.4 - - - -
45E ARG 2.9 20.1 + - - -
46E THR* 2.4 35.9 + - - +
111E ILE* 1.3 81.6 - - - +
113E GLY* 1.3 59.0 + - - +
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Residues in contact with GLY 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D PHE* 3.4 20.4 - - - -
18E LEU* 3.8 1.4 - - - -
19E PHE* 2.8 36.1 + - - +
43E SER 3.2 13.0 - - - -
44E LEU* 4.3 1.8 - - - -
45E ARG* 3.9 4.9 - - - -
112E SER* 1.3 78.4 - - - +
114E GLN* 1.3 64.3 + - - -
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Residues in contact with GLN 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D PHE* 3.5 23.1 - - + -
93D GLU* 2.9 56.3 + - - +
16E ASN* 3.2 16.3 + - - +
17E TYR 3.4 7.4 - - - +
18E LEU* 5.9 0.2 - - - -
19E PHE* 4.1 0.4 - - - -
41E GLN 3.7 0.5 - - - +
42E LEU* 3.2 9.2 - - - +
43E SER* 2.8 44.2 + - - +
45E ARG* 3.8 16.4 - - + +
113E GLY* 1.3 73.6 - - - -
115E HIS* 1.3 59.4 + - - +
116E LEU* 3.6 23.7 + - + +
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Residues in contact with HIS 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D TYR* 3.1 53.8 - + + -
16E ASN* 3.4 3.3 - - - -
17E TYR* 2.7 49.6 + - + +
18E LEU 4.8 1.8 - - - +
19E PHE* 4.0 15.4 - - + +
31E PHE* 3.3 33.3 - + + -
34E ASP* 4.9 0.7 - - - -
40E HIS* 2.9 27.0 + - + -
41E GLN 3.6 7.4 - - - -
42E LEU* 4.3 2.7 - - + -
114E GLN* 1.3 71.2 - - - +
116E LEU* 1.3 73.6 + - - +
117E VAL* 3.7 7.0 - - + +
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Residues in contact with LEU 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E PRO* 4.5 9.9 - - + +
15E GLN 3.7 4.9 - - - +
16E ASN* 3.3 31.4 - - + -
40E HIS* 3.1 5.0 - - - -
41E GLN* 2.6 58.3 + - + +
43E SER* 3.8 22.9 - - - +
93E GLU* 5.5 5.4 - - + +
114E GLN* 3.6 20.0 - - + +
115E HIS* 1.3 75.3 - - - +
117E VAL* 1.3 62.3 + - - +
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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