Contacts of the strand formed by residues 27 - 35 (chain B) in PDB entry 4LGD
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 PHE 27 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B LEU* 5.3 1.3 - - + -
14B LEU* 4.0 14.4 - - + -
23B PRO* 2.8 15.0 + - + +
24B GLU* 3.0 24.4 - - - +
26B VAL* 1.3 100.5 - - + +
28B ASP* 1.3 62.0 + - - +
29B VAL* 4.0 6.7 + - + +
44B ALA* 4.3 4.5 - - + -
45B ILE 3.2 15.9 - - - -
46B HIS* 3.7 25.4 - - + -
47B LYS* 3.7 6.1 - - - -
53B VAL* 3.6 29.4 - - + -
55B ILE* 4.0 20.2 - - + -
89B TYR* 3.9 26.2 - + - -
96B TRP* 5.6 0.9 - + + -
98B VAL* 3.7 20.4 - - + -
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Residues in contact with ASP 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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24B GLU 5.0 0.2 - - - +
27B PHE* 1.3 71.6 - - - +
29B VAL* 1.3 60.7 + - - +
30B LEU* 2.9 16.2 - - + +
44B ALA* 3.0 1.6 - - - -
45B ILE* 2.8 49.6 + - + +
47B LYS* 3.3 32.4 + - - +
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Residues in contact with VAL 29 (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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24B GLU* 5.8 3.8 - - + -
27B PHE* 4.0 7.3 + - + +
28B ASP* 1.3 73.9 - - - +
30B LEU* 1.3 72.5 + - - +
42B PHE* 4.0 30.7 - - + -
43B LYS 3.9 2.5 - - - +
44B ALA* 4.0 10.1 - - + -
55B ILE* 4.8 4.5 - - + -
57B GLN* 5.3 4.9 - - - +
96B TRP* 4.1 30.7 - - + -
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Residues in contact with LEU 30 (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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28B ASP* 2.9 35.0 - - + +
29B VAL* 1.3 87.7 - - - +
31B GLU* 1.3 84.2 + - - +
32B LYS 3.7 0.5 + - - -
42B PHE* 3.9 4.0 - - - -
43B LYS* 2.6 38.7 + - + +
44B ALA* 3.9 0.9 - - - -
45B ILE* 3.7 35.0 - - + -
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Residues in contact with GLU 31 (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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30B LEU* 1.3 98.5 - - - +
32B LYS* 1.3 68.4 + - - +
33B LEU* 4.3 11.7 - - + +
42B PHE* 3.9 0.7 - - - -
43B LYS* 2.9 57.2 + - - +
101B TYR* 5.4 0.3 + - - -
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Residues in contact with LYS 32 (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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30B LEU 3.7 0.4 + - - -
31B GLU* 1.3 78.4 - - - +
33B LEU* 1.3 65.8 + - - +
34B GLY* 3.5 30.9 + - - +
35B GLU* 3.1 29.0 + - - -
40B SER* 3.6 11.0 + - - -
41B VAL 4.1 1.3 - - - +
42B PHE* 3.5 34.4 - - + -
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Residues in contact with LEU 33 (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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31B GLU* 4.3 13.2 - - + +
32B LYS* 1.3 77.7 - - - +
34B GLY* 1.3 57.7 + - - +
41B VAL* 3.0 34.3 + - + +
42B PHE 4.0 2.2 - - - +
43B LYS* 3.8 33.2 - - + +
54B ALA* 4.9 1.8 - - + -
101B TYR* 3.7 34.8 - - + +
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Residues in contact with GLY 34 (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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32B LYS* 3.4 21.8 - - - +
33B LEU* 1.3 79.8 - - - +
35B GLU* 1.3 69.5 + - - +
40B SER* 3.7 0.5 - - - -
41B VAL* 3.3 21.2 + - - +
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Residues in contact with GLU 35 (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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32B LYS* 3.1 24.1 + - - -
34B GLY* 1.3 78.1 - - - +
36B GLY* 1.3 64.3 + - - +
39B GLY 3.5 12.4 - - - +
40B SER* 3.4 18.3 + - - +
41B VAL* 4.6 3.1 - - - +
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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