Contacts of the strand formed by residues 70 - 75 (chain A) in PDB entry 4U6Q
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 ALA 70 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LEU* 3.6 19.6 - - + +
31A ALA* 4.5 2.9 - - + -
66A VAL* 2.8 41.9 + - + +
67A LEU 5.2 1.0 - - - +
68A ASN 3.8 0.2 - - - -
69A GLU* 1.3 69.7 - - - +
71A VAL* 1.3 59.9 + - - +
72A GLY 4.2 11.0 - - - +
73A ALA* 5.9 0.9 - - + -
89A PHE* 4.8 11.4 - - + -
91A ALA* 3.1 4.0 + - - +
92A LEU* 3.0 28.7 + - + +
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Residues in contact with VAL 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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28A PRO* 3.8 29.6 - - + -
29A LEU 2.8 11.8 + - - +
30A VAL* 6.0 0.4 - - + -
69A GLU 3.5 12.8 - - - +
70A ALA* 1.3 74.3 - - - +
72A GLY* 1.3 57.9 + - - +
91A ALA* 3.4 18.6 - - + +
92A LEU* 3.8 1.1 - - - -
93A ARG* 2.7 40.7 + - + +
94A ILE* 3.5 6.4 + - + +
339A ILE* 5.6 8.3 - - + -
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Residues in contact with GLY 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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29A LEU 3.3 5.8 + - - +
30A VAL* 3.4 16.6 - - - +
31A ALA 3.0 22.4 + - - -
70A ALA* 4.2 4.9 - - - +
71A VAL* 1.3 80.4 - - - +
73A ALA* 1.3 60.4 + - - +
92A LEU* 3.5 4.6 - - - +
94A ILE* 3.4 19.1 - - - -
335A ILE* 4.8 3.1 - - - -
339A ILE* 6.6 0.4 - - - -
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Residues in contact with ALA 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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31A ALA* 3.3 9.6 - - + +
33A LEU* 4.2 24.9 - - + -
70A ALA* 5.9 0.7 - - + -
72A GLY* 1.3 75.7 - - - +
74A LEU* 1.3 63.7 + - - +
81A LEU* 6.1 0.4 - - + -
89A PHE* 5.3 2.7 - - + -
92A LEU* 3.7 21.5 - - + -
94A ILE 3.0 8.1 + - - +
95A ILE* 3.4 9.9 - - + +
96A VAL* 2.9 27.2 + - - -
335A ILE* 4.1 4.6 - - - +
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Residues in contact with LEU 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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30A VAL* 4.1 18.8 - - + -
31A ALA 2.8 8.8 + - - +
32A LEU* 3.3 18.8 - - + +
33A LEU* 2.9 26.6 + - - +
38A CYS* 6.3 1.3 - - - -
41A GLU* 4.2 24.0 - - + -
45A LEU* 4.7 7.4 - - + -
51A VAL* 6.1 3.4 - - + -
73A ALA* 1.3 75.0 - - - +
75A MET* 1.3 62.3 + - - +
96A VAL* 3.6 13.2 - - + +
98A ILE* 4.0 14.8 - - + -
331A ALA* 3.8 28.7 - - + +
332A ALA* 5.3 0.7 - - - -
335A ILE* 3.6 26.9 - - + -
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Residues in contact with MET 75 (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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32A LEU* 4.7 1.3 - - - -
33A LEU* 4.1 15.9 - - + -
34A ASP* 3.3 11.4 - - - +
74A LEU* 1.3 76.8 - - - +
76A TYR* 1.3 66.1 + - - +
79A ILE* 3.4 23.8 - - + +
81A LEU* 3.5 30.1 - - + -
95A ILE* 3.8 25.8 - - + -
96A VAL 3.3 6.6 + - - +
97A ARG* 3.0 9.9 + - - -
98A ILE* 2.9 26.6 + - - +
104A ASN* 3.3 30.3 - - - +
105A ILE* 3.9 15.9 - - + -
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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