Contacts of the strand formed by residues 43 - 49 (chain A) in PDB entry 4C8B
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 GLN 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A SER* 5.8 4.6 - - - -
35A ALA 3.3 8.7 + - - +
36A ARG* 3.7 42.4 + - + +
42A VAL* 1.3 80.0 - - - +
44A VAL* 1.3 67.1 + - - +
82A LEU* 5.1 0.3 - - - +
96A GLU* 4.9 2.1 - - - -
97A TYR* 3.8 47.3 + - + +
99A PRO* 5.3 4.7 - - - +
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Residues in contact with VAL 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 4.2 13.0 - - + -
34A SER* 3.4 5.7 - - - -
35A ALA* 2.8 53.3 + - + +
36A ARG 4.4 0.4 - - - +
37A HIS* 4.5 12.6 - - + +
40A TRP* 5.1 2.7 - - + -
42A VAL* 4.1 13.7 - - + +
43A GLN* 1.3 81.9 - - - +
45A ALA* 1.3 63.4 + - - +
46A VAL* 5.4 1.3 - - + -
82A LEU* 3.9 22.0 - - + -
94A VAL* 3.7 19.1 - - + -
95A THR 3.5 9.4 - - - +
97A TYR* 3.6 11.7 - - - +
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Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 5.2 0.7 - - + -
32A VAL* 4.7 3.6 - - + -
33A SER 3.4 7.9 - - - +
34A SER* 4.6 0.7 - - - +
44A VAL* 1.3 75.7 - - - +
46A VAL* 1.3 61.3 - - - +
94A VAL* 3.3 7.4 - - - +
95A THR* 2.9 40.4 + - - +
96A GLU 3.9 0.7 - - - +
97A TYR* 3.9 5.5 - - + +
1000A 0LI 3.4 46.9 - - + +
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Residues in contact with VAL 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 4.4 11.4 - - + -
21A LEU* 4.4 13.2 - - + -
31A THR 3.5 1.9 - - - +
32A VAL* 3.4 2.6 - - - -
33A SER* 2.8 57.2 + - - +
35A ALA* 4.7 8.1 - - + -
44A VAL* 5.4 0.9 - - + -
45A ALA* 1.3 75.8 - - - +
47A LYS* 1.3 68.2 + - - +
48A HIS* 3.6 6.2 - - + -
85A CYS* 5.0 0.7 - - - -
90A PHE* 4.1 26.0 - - + -
92A GLY* 4.9 1.1 - - - -
93A ILE 3.2 12.3 - - - +
94A VAL* 4.3 17.5 - - + -
1000A 0LI 3.8 3.4 - - - -
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Residues in contact with LYS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLY 5.6 4.5 - - - +
31A THR 3.4 8.3 - - - +
32A VAL* 4.5 11.0 - - + +
46A VAL* 1.3 72.0 - - - +
48A HIS* 1.3 62.2 + - - +
49A LEU 4.3 0.5 + - - -
63A VAL* 5.6 5.9 - - + +
66A GLU* 2.8 37.6 + - - +
92A GLY* 2.9 23.8 - - - -
93A ILE* 2.8 17.3 + - + +
164A ASP 3.3 20.8 + - - -
165A PHE* 4.1 24.5 - - - +
1000A 0LI 3.4 30.6 - - + +
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Residues in contact with HIS 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 4.8 6.3 - - + +
30A GLY* 4.5 0.9 - - - -
31A THR* 3.0 56.4 + - + -
33A SER* 2.7 26.7 + - - -
46A VAL* 3.6 17.3 - - + -
47A LYS* 1.3 75.0 - - - +
49A LEU* 1.3 66.5 + - - +
50A HIS* 4.0 1.2 + - - -
90A PHE* 3.4 44.2 - + + -
91A LEU 3.2 11.9 - - - +
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A SER* 3.8 21.3 - - - +
30A GLY* 4.3 1.3 - - - -
47A LYS* 4.2 1.2 + - - +
48A HIS* 1.3 77.2 + - - +
50A HIS* 1.3 69.9 + - - +
51A ILE* 3.7 13.9 + - - +
56A LEU* 5.5 1.3 - - + -
59A GLU* 4.9 13.2 - - + -
63A VAL* 4.9 11.5 - - + +
91A LEU* 3.2 27.7 + - + +
92A GLY* 5.0 0.2 - - - -
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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