Contacts of the strand formed by residues 23 - 28 (chain B) in PDB entry 4LL4
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 23 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ALA* 5.5 2.7 - - + +
15B LEU* 5.3 14.1 - - + -
18B ALA* 4.6 7.0 - - + -
21B LYS 4.1 7.0 - - - +
22B LEU* 1.3 79.9 - - - +
24B VAL* 1.3 60.9 + - - +
25B VAL* 4.7 2.7 - - + -
53B ILE* 3.1 37.0 - - + +
55B LEU* 3.6 24.7 - - + -
78B GLN 3.4 2.3 - - - +
79B PHE* 3.3 5.3 - - - -
80B PHE* 2.8 56.6 + - + +
83B GLY* 6.1 1.6 - - - +
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Residues in contact with VAL 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B VAL* 1.3 75.4 - - - +
25B VAL* 1.3 66.0 + - - +
42B PHE* 3.8 17.7 - - + -
52B VAL* 4.6 7.1 - - + +
53B ILE 2.9 4.9 + - - +
54B PHE* 3.4 43.1 - - + -
55B LEU 3.0 23.9 + - - -
77B PHE* 4.3 4.7 - - + -
78B GLN 3.4 4.0 - - - -
79B PHE* 3.4 41.7 - - + -
97B LEU* 4.0 8.5 - - + -
101B ILE* 4.8 4.5 - - + -
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Residues in contact with VAL 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B PHE* 4.3 10.8 - - + -
23B VAL* 4.6 2.5 - - + +
24B VAL* 1.3 81.5 - - - +
26B ASP* 1.3 62.5 + - - +
27B PHE* 3.6 27.9 + - + -
55B LEU* 3.4 27.4 - - + +
57B VAL* 3.9 25.8 - - + -
76B THR 3.4 2.1 - - - +
77B PHE* 3.1 12.0 - - - -
78B GLN 2.9 27.7 + - - +
80B PHE* 3.8 27.8 - - + -
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Residues in contact with ASP 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B VAL* 1.3 73.1 - - - +
27B PHE* 1.3 63.3 + - - +
28B SER* 3.2 27.2 + - - -
35B ALA* 5.1 0.3 - - - +
38B ILE* 4.1 11.4 - - - +
39B LYS* 4.9 4.5 - - - +
42B PHE* 3.6 31.1 - - + +
55B LEU 2.9 8.9 + - - +
56B GLU* 3.4 10.7 - - + +
57B VAL 2.8 26.7 + - - -
75B PRO* 4.4 6.9 - - - +
77B PHE* 3.4 34.5 - - + -
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Residues in contact with PHE 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B PHE* 4.8 5.8 - + - -
25B VAL* 3.6 25.4 - - + -
26B ASP* 1.3 70.7 - - - +
28B SER* 1.3 61.8 + - - +
57B VAL* 3.3 31.0 - - + -
59B VAL* 4.0 13.9 - - + -
65B VAL* 4.2 16.8 - - + -
66B ALA* 4.5 7.6 - - - -
69B CYS* 3.7 29.2 - - + -
71B VAL* 3.8 29.8 - - + -
74B MET* 3.8 6.1 - - - +
75B PRO* 3.6 4.5 - - - +
76B THR* 3.1 38.7 + - - +
78B GLN* 3.8 28.5 - - + -
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Residues in contact with SER 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ASP* 3.2 18.2 - - - -
27B PHE* 1.3 73.1 - - - +
29B ALA* 1.3 76.6 + - - +
35B ALA* 4.0 16.4 + - - +
39B LYS* 4.6 6.8 - - - +
56B GLU* 3.2 28.4 + - - -
57B VAL 2.8 11.2 + - - -
58B ASP* 3.7 4.1 + - - -
59B VAL* 3.1 27.5 + - - +
74B MET* 3.9 3.4 - - - -
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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