Contacts of the strand formed by residues 47 - 57 (chain E) in PDB entry 6S7T
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 47 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41E ASP 3.4 6.5 - - - +
42E LEU* 3.6 26.7 - - + +
46E LEU* 1.3 70.4 - - - +
48E LYS* 1.3 60.4 + - - +
49E VAL* 4.1 4.9 - - + -
134E VAL* 3.6 1.0 - - - -
135E TYR* 2.8 47.7 + - + +
138E VAL* 3.7 22.7 - - + +
139E LEU* 5.0 0.7 - - + -
156E PHE* 4.1 9.2 - - + -
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Residues in contact with LYS 48 (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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39E THR 3.6 2.6 - - - +
41E ASP* 2.8 59.9 + - + +
44E SER* 2.7 36.6 + - - -
46E LEU* 3.7 11.6 + - + +
47E ALA* 1.3 74.9 - - - +
49E VAL* 1.3 61.5 + - - +
50E THR* 5.0 3.8 + - - +
133E THR 3.4 7.0 - - - +
134E VAL* 3.7 30.3 - - + -
362E GLU* 3.7 9.8 + - + -
419E GLN* 4.6 8.7 - - - +
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Residues in contact with VAL 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E ARG* 4.3 19.1 - - + +
39E THR 3.2 4.5 - - - +
40E VAL* 3.7 31.2 - - + -
47E ALA* 4.5 6.1 - - + +
48E LYS* 1.3 77.6 - - - +
50E THR* 1.3 63.0 + - - +
51E ALA* 5.5 3.4 - - + +
131E VAL 3.8 1.4 - - - +
132E GLU* 3.5 1.4 - - - -
133E THR* 2.9 50.2 + - + +
135E TYR* 4.1 25.1 - - + +
156E PHE* 5.7 5.2 - - + -
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Residues in contact with THR 50 (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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37E LYS 3.6 2.3 - - - +
38E ARG* 3.1 3.3 - - - -
39E THR* 2.9 38.3 + - - -
48E LYS* 5.0 3.6 + - - +
49E VAL* 1.3 74.3 + - - +
51E ALA* 1.3 63.0 + - - +
52E GLU* 4.2 8.1 + - + +
130E ILE* 3.8 15.3 - - + -
131E VAL 3.4 3.4 - - - -
132E GLU* 3.4 36.5 - - + +
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Residues in contact with ALA 51 (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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36E VAL* 4.5 1.3 - - + -
37E LYS 3.4 5.2 - - - +
38E ARG* 3.9 15.0 - - + +
49E VAL* 4.3 3.3 - - + -
50E THR* 1.3 73.7 - - - +
52E GLU* 1.3 63.0 + - - +
53E VAL* 3.5 9.5 + - + +
130E ILE* 3.5 2.2 - - - -
131E VAL* 2.8 43.7 + - + +
162E PHE* 3.6 32.8 - - + -
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Residues in contact with GLU 52 (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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35E ASP 3.4 3.2 - - - +
36E VAL* 3.1 6.1 - - - -
37E LYS* 2.9 60.8 + - + +
50E THR* 5.0 7.8 - - + +
51E ALA* 1.3 71.2 - - - +
53E VAL* 1.3 58.7 + - - +
54E VAL* 4.3 3.1 - - + -
129E VAL 3.6 7.0 - - - +
130E ILE* 4.4 26.1 - - + +
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Residues in contact with VAL 53 (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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33E ASN* 3.5 33.2 - - + +
35E ASP 3.8 2.9 - - - -
36E VAL* 3.6 17.5 - - + -
51E ALA* 3.5 9.4 + - + +
52E GLU* 1.3 76.4 - - - +
54E VAL* 1.3 64.8 + - - +
55E LEU* 3.8 15.1 + - + -
69E PHE* 6.2 1.1 - - + -
129E VAL* 2.9 47.2 + - + +
131E VAL* 5.3 2.7 - - + -
162E PHE* 3.6 33.7 - - + -
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Residues in contact with VAL 54 (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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33E ASN* 3.2 4.9 - - - +
34E GLU* 2.9 30.7 + - + +
35E ASP* 3.4 27.3 + - + +
52E GLU* 5.4 2.0 - - + +
53E VAL* 1.3 76.1 - - - +
55E LEU* 1.3 60.9 + - - +
56E ALA 3.5 0.2 + - - -
126E LYS* 3.7 36.3 - - + +
127E ILE 3.2 12.8 - - - +
128E SER* 3.8 21.3 - - - +
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Residues in contact with LEU 55 (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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31E LEU* 4.3 23.3 - - + -
32E ILE 4.0 2.5 - - - +
33E ASN* 4.3 12.6 - - + +
53E VAL* 3.8 19.9 + - + -
54E VAL* 1.3 70.3 - - - +
56E ALA* 1.3 59.3 + - - +
69E PHE* 3.4 57.9 - - + -
117E LEU* 5.0 0.9 - - + -
121E LEU* 4.2 4.0 - - + +
125E ALA 3.8 1.4 - - - +
126E LYS* 3.3 4.9 - - - -
127E ILE* 2.9 54.9 + - + +
129E VAL* 4.8 5.8 - - + -
166E TYR* 5.2 9.6 - - + -
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Residues in contact with ALA 56 (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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31E LEU* 3.1 5.8 - - - +
32E ILE* 2.8 36.6 + - + +
34E GLU* 3.2 41.3 - - + +
54E VAL 3.5 0.8 + - - -
55E LEU* 1.3 73.5 - - - +
57E HIS* 1.3 62.1 + - - +
58E LEU* 4.0 1.6 + - + -
121E LEU* 4.9 0.9 - - - -
125E ALA 3.7 5.8 - - - +
126E LYS* 3.8 13.7 - - + -
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Residues in contact with HIS 57 (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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29E PRO* 3.0 33.3 - - + +
30E PRO* 4.1 13.3 + - + -
31E LEU* 3.9 11.7 - - + -
56E ALA* 1.3 73.8 - - - +
58E LEU* 1.3 91.3 + - - +
59E GLY 3.3 0.7 + - - -
60E GLY 4.9 5.8 - - - -
63E THR* 4.0 17.1 + - - -
66E ALA* 3.9 21.7 - - + +
121E LEU* 4.0 18.6 - - + +
122E ASP 4.3 2.5 - - - +
123E PRO* 3.4 33.7 - - + +
124E GLY* 3.2 20.2 + - - +
125E ALA 3.7 6.4 + - - +
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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