Contacts of the strand formed by residues 69 - 74 (chain A) in PDB entry 2HEI
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 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A CYS* 3.3 7.4 - - + +
21A PHE* 3.6 35.2 - - + -
61A SER* 3.1 4.0 - - - -
62A VAL* 2.8 42.0 + - - +
64A LEU* 3.6 31.6 - - + -
68A THR* 1.3 76.3 - - - +
70A LYS* 1.3 61.4 + - - +
71A PHE* 3.9 26.9 + - + -
178A ALA* 3.9 20.0 - - + +
183A LYS* 5.9 0.7 - - - -
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Residues in contact with LYS 70 (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 ILE* 3.8 33.6 - - + +
19A CYS 2.8 13.6 + - - +
20A GLN* 3.2 19.7 - - + +
21A PHE* 2.9 29.3 + - - +
59A THR* 3.4 31.0 - - + -
60A GLN 3.7 0.2 - - - -
61A SER* 3.5 20.6 - - - +
68A THR 4.1 0.2 + - - -
69A VAL* 1.3 73.1 - - - +
71A PHE* 1.3 59.9 + - - +
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Residues in contact with PHE 71 (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 PHE* 3.5 10.5 - - + -
23A LEU* 3.9 31.4 - - + -
40A PHE* 4.1 6.5 - + - -
58A LEU 3.6 1.2 - - - +
59A THR* 3.1 29.5 - - - +
60A GLN 2.8 23.0 + - - +
62A VAL* 4.2 10.1 - - + -
69A VAL* 3.9 22.4 - - + -
70A LYS* 1.3 76.0 - - - +
72A GLU* 1.3 59.0 + - - +
73A ILE* 3.7 19.6 + - + +
95A ALA* 5.0 0.9 - - + -
174A PHE* 3.5 44.2 - + + -
177A ILE* 4.2 4.5 - - + -
178A ALA* 3.9 10.8 - - + -
181A LEU* 3.7 24.0 - - + -
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Residues in contact with GLU 72 (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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20A GLN* 3.7 24.3 + - - +
21A PHE 2.9 8.9 + - - +
22A LYS* 3.4 10.9 - - - +
23A LEU 2.9 25.1 + - - +
57A PHE* 3.4 47.3 - - + -
58A LEU 3.6 2.9 - - - -
59A THR* 4.0 8.4 + - + +
71A PHE* 1.3 69.7 - - - +
73A ILE* 1.3 58.4 + - - +
74A TRP* 2.9 29.3 + - - +
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Residues in contact with ILE 73 (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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23A LEU* 3.3 9.6 - - + +
25A LEU* 3.4 32.8 - - + -
37A VAL* 3.7 20.2 - - + -
40A PHE* 3.7 33.7 - - + -
41A VAL* 4.0 16.2 - - + -
53A ILE* 4.0 5.0 - - - +
57A PHE* 3.2 6.2 - - - +
58A LEU 2.7 36.7 + - - +
60A GLN 4.9 0.4 - - - +
71A PHE* 3.7 18.6 - - + +
72A GLU* 1.3 75.3 - - - +
74A TRP* 1.3 63.3 + - - +
174A PHE* 3.8 15.0 - - + -
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Residues in contact with TRP 74 (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 LYS* 3.5 41.6 - - + +
23A LEU 2.8 11.8 + - - +
24A VAL* 3.5 11.1 - - + +
25A LEU* 2.8 30.7 + - - +
56A ALA 4.7 3.4 - - - +
57A PHE* 3.6 26.6 - + + -
72A GLU* 2.9 36.4 + - - -
73A ILE* 1.3 79.5 - - - +
75A ASP* 1.3 60.6 + - - +
88A MET* 4.2 18.6 - - + -
89A TYR* 3.7 31.2 - + + -
91A ARG* 6.4 0.2 - - - -
124B PRO* 3.5 38.8 - - + -
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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