Contacts of the strand formed by residues 41 - 48 (chain A) in PDB entry 2H6D
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 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A ILE* 3.3 28.0 - - + -
33A GLY 3.2 10.8 - - - +
34A GLU* 3.6 28.3 + - + -
39A GLY* 3.4 16.3 + - - +
40A HIS* 1.3 96.2 + - - +
42A VAL* 1.3 63.6 + - - +
80A TYR* 5.7 0.2 - - - -
95A TYR* 3.4 43.8 + - + +
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Residues in contact with VAL 42 (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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16A TYR* 3.7 45.1 - - + +
32A ILE* 3.5 9.5 - - - +
33A GLY* 2.9 31.2 + - - +
40A HIS* 4.0 7.6 - - - +
41A LYS* 1.3 79.0 - - - +
43A ALA* 1.3 61.2 + - - +
44A VAL* 3.8 22.7 - - + -
80A TYR* 4.1 11.9 - - + -
92A VAL* 3.9 20.9 - - + -
93A MET 3.3 13.7 - - - +
95A TYR* 3.8 7.9 - - - +
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Residues in contact with ALA 43 (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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22A LEU* 4.4 7.9 - - + -
30A VAL* 4.0 11.7 - - + -
31A LYS 3.6 4.7 - - - -
32A ILE* 4.7 0.9 - - - +
42A VAL* 1.3 74.7 - - - +
44A VAL* 1.3 58.3 + - - +
45A LYS 3.9 0.2 - - - -
91A MET 3.5 0.3 - - - +
93A MET* 2.7 44.2 + - - +
94A GLU 3.7 8.7 - - - +
95A TYR* 4.0 7.5 - - + +
158A PHE* 3.6 34.5 - - + -
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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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13A ILE* 3.8 26.7 - - + -
16A TYR* 5.7 0.7 - - + -
18A LEU* 3.7 26.2 - - + -
29A LYS 3.7 0.2 - - - +
30A VAL* 3.2 3.9 - - - +
31A LYS 2.7 42.9 + - - +
33A GLY 4.7 0.7 - - - +
42A VAL* 3.8 22.4 - - + -
43A ALA* 1.3 73.9 - - - +
45A LYS* 1.3 62.7 + - - +
46A ILE* 3.6 11.5 + - + +
90A PHE* 4.1 22.2 - - + -
91A MET 3.3 9.6 - - - +
92A VAL* 4.6 8.1 - - + -
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Residues in contact with LYS 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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28A GLY 5.9 0.4 - - - -
29A LYS 3.5 10.3 - - - +
30A VAL* 4.0 12.8 - - + -
43A ALA 3.8 1.8 + - - -
44A VAL* 1.3 70.7 - - - +
46A ILE* 1.3 62.0 + - - +
47A LEU* 3.9 25.3 + - + -
89A PHE 3.5 1.9 - - - +
90A PHE* 3.5 3.6 - - - -
91A MET* 2.8 62.5 + - + +
93A MET* 3.2 31.6 - - + +
157A ASP* 2.7 43.5 + - - +
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Residues in contact with ILE 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* 3.9 27.4 - - + -
28A GLY* 3.3 6.6 - - - -
29A LYS* 2.7 39.0 + - + +
31A LYS* 3.9 27.4 - - + +
44A VAL* 4.0 9.9 - - + +
45A LYS* 1.3 75.3 - - - +
47A LEU* 1.3 64.6 + - - +
48A ASN* 4.0 1.9 + - + +
88A ASP* 3.8 20.4 - - - +
89A PHE 3.4 4.5 - - - +
90A PHE* 3.8 31.6 - - + -
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Residues in contact with LEU 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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27A PHE* 3.5 35.7 - - + +
28A GLY* 4.4 0.9 - - - +
45A LYS* 4.0 24.7 - - + +
46A ILE* 1.3 74.7 - - - +
48A ASN* 1.3 63.7 + - - +
49A ARG 3.5 0.7 + - - -
52A ILE* 4.6 7.4 - - + -
61A ILE* 3.7 32.3 - - + -
65A ILE* 4.6 1.6 - - + -
88A ASP* 3.3 5.0 - - - -
89A PHE* 2.8 61.4 + - + +
91A MET* 3.8 25.6 - - + -
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Residues in contact with ASN 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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27A PHE 4.3 5.4 + - - +
28A GLY* 5.3 0.8 - - - -
46A ILE* 4.0 3.6 + - + +
47A LEU* 1.3 71.2 - - - +
49A ARG* 1.3 64.3 + - - +
50A GLN* 2.9 41.8 + - - +
51A LYS* 3.1 23.1 + - + +
52A ILE* 3.1 21.9 + - - +
87A THR* 3.7 2.4 + - - -
88A ASP* 3.3 22.1 + - - +
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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