Contacts of the strand formed by residues 5 - 13 (chain E) in PDB entry 1SEJ
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 ASN 5 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4E LYS* 1.3 78.7 - - - +
6E VAL* 1.3 62.5 + - - +
7E SER* 3.0 27.5 + - - -
108E GLU 4.6 2.2 + - - -
109E ASN* 4.0 16.5 + - - +
110E ILE* 2.8 31.9 + - - +
129E ASP* 3.1 21.9 - - - +
130E ARG* 3.3 26.0 + - - +
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Residues in contact with VAL 6 (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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4E LYS 4.8 4.3 - - - +
5E ASN* 1.3 76.9 - - - +
7E SER* 1.3 61.3 + - - +
98E ILE* 4.8 15.9 - - + -
101E LEU* 4.9 7.6 - - + -
110E ILE* 3.4 32.1 - - + -
112E VAL* 3.8 26.5 - - + -
127E PHE 3.3 26.2 - - - +
128E VAL* 3.6 10.2 - - + -
129E ASP* 2.7 41.0 + - - +
130E ARG 3.3 2.9 + - - -
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Residues in contact with SER 7 (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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5E ASN* 3.0 23.4 + - - -
6E VAL* 1.3 73.4 - - - +
8E ILE* 1.3 62.8 + - - +
110E ILE 2.9 8.0 + - - -
111E PHE* 3.1 23.5 - - - +
112E VAL 2.8 24.1 + - - -
128E VAL* 4.7 0.7 - - - -
130E ARG* 3.3 23.4 + - - +
132E TYR* 3.7 24.4 - - - -
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Residues in contact with ILE 8 (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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7E SER* 1.3 73.2 - - - +
9E VAL* 1.3 60.8 + - - +
10E VAL* 3.9 18.2 - - + -
112E VAL* 3.6 24.9 - - + -
119E TYR* 3.7 27.8 - - + -
122E ALA* 4.6 1.6 - - + -
123E LEU* 3.4 35.7 - - + -
128E VAL* 3.9 21.8 - - + -
130E ARG 2.8 13.8 + - - +
131E ILE* 4.0 9.0 - - + -
132E TYR* 2.6 36.0 + - - +
147E PHE* 3.9 10.5 - - + -
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Residues in contact with VAL 9 (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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7E SER 4.3 0.7 - - - +
8E ILE* 1.3 80.0 - - - +
10E VAL* 1.3 57.6 + - - +
35E PHE* 5.3 1.8 - - + -
36E PHE* 3.9 20.4 - - + -
39E ILE* 4.1 16.8 - - + -
40E THR* 4.0 10.1 - - + -
111E PHE* 3.4 37.0 - - + -
112E VAL 3.3 9.5 + - - +
113E CYS* 4.3 1.7 - - - -
119E TYR* 2.6 24.9 + - - -
132E TYR* 3.5 13.2 - - + +
621E F89 3.4 31.9 - - + +
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Residues in contact with VAL 10 (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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8E ILE* 3.9 5.2 - - + -
9E VAL* 1.3 73.8 - - - +
11E ALA* 1.3 70.6 + - - +
12E ALA 4.6 0.2 - - - +
19E ILE* 3.8 20.9 - - + -
119E TYR* 3.0 34.5 - - + +
131E ILE* 4.7 0.7 - - + -
132E TYR 3.0 15.6 + - - +
133E LEU* 3.7 10.9 - - + +
134E THR 2.8 22.2 + - - -
147E PHE* 3.6 39.5 - - + -
621E F89 3.4 9.8 - - - +
622E NDP 3.4 11.9 - - - +
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Residues in contact with ALA 11 (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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10E VAL* 1.3 77.9 - - - +
12E ALA* 1.3 61.3 + - - +
19E ILE* 3.2 6.4 - - - +
27E TRP* 3.5 22.0 - - + +
32E ASP* 3.4 25.6 - - - +
134E THR* 3.1 16.6 - - + +
136E VAL* 4.3 1.1 - - + -
621E F89 3.6 12.1 - - + +
622E NDP 2.8 31.8 + - - +
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Residues in contact with ALA 12 (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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10E VAL* 4.8 0.7 - - + -
11E ALA* 1.3 72.6 - - - +
13E SER* 1.3 67.6 + - - +
14E VAL 3.4 0.2 + - - -
17E SER* 3.5 24.0 - - - +
18E GLY 3.1 5.2 - - - -
19E ILE* 3.3 22.0 - - + -
27E TRP* 3.9 4.5 - - - -
133E LEU* 3.9 13.9 - - + +
134E THR 3.0 7.4 + - - +
135E ARG* 3.5 4.7 - - - +
136E VAL 3.0 17.2 + - - -
147E PHE* 4.1 8.3 - - + -
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Residues in contact with SER 13 (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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12E ALA* 1.3 74.0 - - - +
14E VAL* 1.3 66.3 + - - +
16E SER* 3.4 5.4 + - - -
17E SER* 3.0 22.9 + - - -
18E GLY* 2.7 33.0 + - - -
27E TRP* 3.8 4.4 - - - -
136E VAL* 3.2 10.5 - - - -
138E LEU 3.5 19.5 - - - -
139E GLU* 2.9 23.3 + - - -
143E PHE* 3.6 13.8 - - - -
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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