Contacts of the strand formed by residues 8 - 12 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F ASP 5.3 1.3 - - - +
7F TYR* 1.3 82.0 - - - +
9F PHE* 1.3 68.8 + - - +
10F TRP* 5.0 10.8 - - + +
46F TYR* 5.6 4.7 - - - +
47F PRO* 3.9 18.6 - - + +
49F GLU* 5.8 4.9 - - + -
72F ASP* 3.5 12.6 + - + +
73F VAL* 5.0 3.1 - - + -
74F ALA* 3.9 21.7 + - - +
75F GLY* 4.2 1.4 + - - -
168F VAL* 5.9 1.0 - - - +
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Residues in contact with PHE 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F LYS* 1.3 81.7 - - - +
10F TRP* 1.3 67.1 + - - +
46F TYR* 6.1 0.7 - - + -
47F PRO 3.4 16.1 + - - +
48F VAL* 3.7 7.6 - - + +
49F GLU* 2.8 31.5 + - - +
73F VAL* 5.7 0.2 - - - -
74F ALA 5.2 0.4 - - - +
75F GLY* 4.2 22.4 - - - +
76F VAL 4.3 0.4 - - - -
77F ILE* 3.8 29.2 - - + -
163F TRP* 5.0 5.6 - + - -
164F GLN* 5.1 14.6 - - + -
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Residues in contact with TRP 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F LYS* 5.0 6.0 - - + +
9F PHE* 1.3 86.9 - - - +
11F PHE* 1.3 57.7 + - - +
12F VAL* 5.4 4.1 - - + +
48F VAL* 6.4 0.2 - - - -
49F GLU* 3.4 22.0 - - + +
51F LYS* 4.9 15.3 - - + -
63F PHE* 4.3 18.4 - + + -
66F GLU* 4.2 15.3 - - + -
67F ALA* 3.7 41.7 - - + -
70F ASN* 4.1 27.1 - - + -
73F VAL* 4.0 19.8 - - + +
75F GLY 3.7 11.4 + - - +
76F VAL* 3.5 8.3 - - + +
77F ILE* 2.8 34.3 + - - +
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Residues in contact with PHE 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F TRP* 1.3 74.1 - - - +
12F VAL* 1.3 90.4 + - - +
13F VAL* 4.4 6.3 - - + -
31F ALA* 5.2 7.4 - - + -
34F LEU* 5.4 7.9 - - + -
35F VAL* 3.4 31.9 - - + -
38F LEU* 5.2 11.0 - - + -
48F VAL* 5.2 6.3 - - + -
49F GLU 2.9 16.3 + - - +
50F PHE* 3.7 12.3 - - + -
51F LYS* 3.1 26.9 + - - +
77F ILE* 3.3 27.6 - - + -
79F TRP* 4.0 37.2 - + + -
103F LEU* 5.1 11.2 - - + -
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Residues in contact with VAL 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F TRP* 5.4 4.3 - - + +
11F PHE* 1.3 86.1 - - - +
13F VAL* 1.3 74.1 + - - +
51F LYS* 4.8 1.8 - - + -
52F LEU 4.1 17.0 - - - +
54F ALA* 4.2 12.1 - - + -
60F ILE* 5.0 3.4 - - + -
63F PHE* 3.9 28.3 - - + -
76F VAL* 6.5 1.1 - - + -
77F ILE 3.0 9.4 + - - +
78F THR* 3.9 7.5 + - - +
79F TRP 3.0 27.2 + - - +
89F TRP* 3.6 26.9 - - + -
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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