Contacts of the strand formed by residues 8 - 14 (chain E) in PDB entry 4LQL
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 LYS 8 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6E ASP 4.9 1.1 - - - +
7E TYR* 1.3 75.5 - - - +
9E PHE* 1.3 59.3 + - - +
10E TRP* 4.1 17.3 - - + +
47E PRO 3.9 12.8 - - - +
49E GLU* 5.1 7.4 - - + -
72E ASP* 3.3 29.3 + - + +
73E VAL* 3.6 6.1 - - - +
74E ALA* 2.7 31.9 + - - +
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Residues in contact with PHE 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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8E LYS* 1.3 74.2 - - - +
10E TRP* 1.3 70.6 + - - +
11E PHE* 6.0 0.9 - + - -
46E TYR* 6.2 3.8 - - + -
47E PRO 3.5 9.1 + - - +
48E VAL* 4.3 22.0 - - + -
49E GLU* 2.7 34.8 + - - +
74E ALA* 5.5 1.6 - - + -
75E GLY* 4.4 15.3 - - - +
76E VAL 5.0 0.2 - - - -
77E ILE* 4.0 24.5 - - + -
163E TRP* 5.3 5.4 - + + -
164E GLN* 6.2 3.8 - - + -
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Residues in contact with TRP 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 LYS* 4.1 15.8 - - + +
9E PHE* 1.3 96.3 - - - +
11E PHE* 1.3 64.2 + - - +
12E VAL* 6.0 2.0 - - + -
49E GLU* 3.2 22.8 - - + +
51E LYS* 3.7 44.1 - - + +
63E PHE* 4.6 7.4 - - + -
66E GLU* 4.0 23.3 - - + -
67E ALA* 3.8 27.8 - - + -
70E ASN* 4.6 17.0 - - + -
73E VAL* 3.8 28.3 - - + +
75E GLY 3.8 12.5 + - - +
76E VAL* 4.3 6.5 - - + -
77E ILE 3.7 13.8 + - - -
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Residues in contact with PHE 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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9E PHE* 6.0 0.4 - + - -
10E TRP* 1.3 78.5 - - - +
12E VAL* 1.3 99.9 - - - +
13E VAL* 4.4 4.9 - - + -
31E ALA* 4.6 10.5 - - + -
34E LEU* 4.1 25.1 - - + -
35E VAL* 4.0 27.8 - - + -
48E VAL* 5.9 6.7 - - + -
49E GLU 3.1 13.9 + - - +
50E PHE* 4.1 5.1 - + + +
51E LYS* 3.3 23.6 + - - +
77E ILE* 3.6 36.3 - - + +
79E TRP* 4.2 31.0 - + + -
103E LEU* 5.1 8.1 - - + -
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Residues in contact with VAL 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 TRP* 6.0 2.0 - - + -
11E PHE* 1.3 90.6 - - - +
13E VAL* 1.3 65.1 + - - +
14E GLY 3.5 2.6 + - - -
51E LYS* 5.4 2.7 - - + -
52E LEU 4.2 12.6 - - - +
54E ALA* 4.5 10.1 - - + -
63E PHE* 4.1 30.3 - - + -
77E ILE 4.0 2.2 + - - +
78E THR* 4.1 23.1 - - - -
79E TRP 3.5 17.5 + - - +
89E TRP* 4.1 19.9 - - + -
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Residues in contact with VAL 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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11E PHE* 4.8 4.5 - - + -
12E VAL* 1.3 72.4 - - - +
14E GLY* 1.3 65.8 + - - +
15E SER* 3.2 6.1 + - - -
27E VAL* 3.9 28.5 - - + +
28E GLU* 5.6 1.1 - - - -
31E ALA* 3.6 35.0 - - + +
32E ARG* 5.9 1.3 - - + -
50E PHE* 5.0 11.0 - - + -
51E LYS 5.5 0.2 - - - +
52E LEU 4.1 10.7 + - - +
53E VAL* 4.2 8.1 - - + +
54E ALA* 3.3 19.9 + - - -
79E TRP* 3.9 5.2 - - + -
81E HIS* 5.4 3.1 - - + +
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Residues in contact with GLY 14 (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 VAL 3.5 3.0 + - - -
13E VAL* 1.3 70.7 - - - +
15E SER* 1.3 57.1 + - - -
54E ALA* 3.9 9.4 - - - -
79E TRP 3.2 13.5 + - - -
80E MET* 3.8 18.6 - - - -
81E HIS* 2.7 34.5 + - - +
82E THR 3.4 1.9 + - - -
84E SER* 3.3 13.0 - - - -
89E TRP* 4.5 4.9 - - - -
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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