Contacts of the strand formed by residues 37 - 43 (chain A) in PDB entry 3A7H
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 GLU 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A LYS* 2.9 33.5 + - + +
31A GLY 3.6 5.2 - - - +
32A LYS* 3.8 24.6 - - + +
36A GLY* 1.3 78.6 - - - +
38A VAL* 1.3 65.5 + - - +
39A PHE* 3.7 26.4 - - + -
52A ILE 3.6 0.9 - - - +
53A LYS* 3.4 3.5 - - - +
54A ILE* 2.9 36.5 + - + +
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Residues in contact with VAL 38 (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 LYS* 3.5 3.6 - - - +
30A ILE* 2.6 43.9 + - + -
31A GLY* 2.8 24.4 + - - +
37A GLU* 1.3 79.0 - - - +
39A PHE* 1.3 64.2 + - - +
51A ALA* 4.6 5.2 - - + -
52A ILE 3.3 9.9 - - - +
53A LYS* 4.2 13.9 - - + -
99A MET* 5.1 0.2 - - + -
400A ATP 3.6 70.7 - - + +
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Residues in contact with PHE 39 (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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26A LYS* 3.7 50.9 - - + -
28A GLU* 3.4 7.2 - - - +
29A LYS* 3.6 39.3 - - + -
30A ILE* 3.8 6.8 - - - +
37A GLU* 3.7 38.1 - - + -
38A VAL* 1.3 79.2 - - - +
40A LYS* 1.3 64.5 - - - +
41A GLY 3.9 0.2 - - - -
51A ALA* 3.3 4.5 - - - -
52A ILE* 2.6 51.9 + - + +
54A ILE* 4.4 13.7 - - + -
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Residues in contact with LYS 40 (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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26A LYS* 3.7 2.3 - - - -
27A LEU* 2.7 42.4 + - + +
28A GLU* 3.0 24.6 + - + +
30A ILE* 3.7 21.4 - - + +
39A PHE* 1.3 74.7 - - - +
41A GLY* 1.3 62.1 + - - +
49A VAL* 3.8 22.0 - - + -
50A VAL 3.8 3.1 - - - -
101A TYR* 3.6 44.4 + - + +
154A GLU* 5.2 7.1 + - - -
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Residues in contact with GLY 41 (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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25A THR 3.1 14.8 - - - -
27A LEU* 4.0 5.8 - - - -
39A PHE 3.9 0.8 + - - -
40A LYS* 1.3 76.6 - - - +
42A ILE* 1.3 60.9 - - - -
49A VAL* 3.4 11.1 - - - +
50A VAL* 2.9 38.4 + - - +
52A ILE* 4.1 11.8 - - - +
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Residues in contact with ILE 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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24A PHE* 3.3 8.2 - - - -
25A THR* 2.9 33.3 + - - +
27A LEU* 3.7 29.4 - - + -
41A GLY* 1.3 72.8 - - - -
43A ASP* 1.3 76.0 + - - +
44A ASN* 3.2 14.4 + - - +
47A GLN* 3.8 37.7 - - - +
48A LYS 3.6 4.5 - - - +
49A VAL* 3.9 28.0 - - + +
50A VAL* 4.2 1.1 - - - +
52A ILE* 5.0 0.4 - - - +
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Residues in contact with ASP 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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23A LEU* 3.9 4.3 - - - +
24A PHE* 3.7 34.1 - - + -
42A ILE* 1.3 70.6 - - - +
44A ASN* 1.3 51.5 + - - +
45A ARG* 2.9 34.4 + - - +
46A THR* 3.5 19.6 + - - +
47A GLN* 2.7 35.5 + - - -
48A LYS* 2.9 17.3 + - + +
50A VAL* 4.3 8.4 - - + +
89A TYR* 5.5 0.3 + - - -
98A ILE* 5.9 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