Contacts of the strand formed by residues 70 - 75 (chain C) in PDB entry 3SDL
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 THR 70 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C THR* 3.3 24.8 - - + +
8C LYS* 3.9 24.6 + - + +
14C GLU* 5.4 0.7 + - - -
48C HIS* 3.1 57.8 + - + +
65C LEU* 3.9 5.4 - - - +
68C GLY 4.2 2.1 + - - -
69C SER* 1.3 74.3 - - - +
71C VAL* 1.3 77.8 + - - +
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Residues in contact with VAL 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C LEU* 3.9 17.5 - - + -
6C THR 2.7 18.1 + - - +
7C VAL* 3.6 25.1 - - + -
8C LYS* 2.8 31.2 + - - +
28C LEU* 4.6 7.4 - - + -
45C LEU* 5.2 6.3 - - + -
46C ALA 3.4 10.5 - - - +
54C LEU* 4.5 10.5 - - + -
65C LEU* 3.4 42.4 - - + -
69C SER 4.1 0.2 + - - -
70C THR* 1.3 76.7 - - - +
72C LEU* 1.3 60.3 + - - +
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Residues in contact with LEU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A PRO* 3.4 28.0 - - + -
97A ILE* 3.8 13.7 - - + -
100A PHE 3.1 24.0 - - - +
101A GLU* 3.5 18.8 - - + +
8C LYS* 3.4 15.9 - - + -
44C ARG 3.4 1.7 - - - +
45C LEU* 3.2 10.2 - - - +
46C ALA* 2.7 44.6 + - + +
47C VAL 4.0 11.7 - - - +
48C HIS* 3.4 33.7 - - + +
51C GLY* 4.6 0.2 - - - -
71C VAL* 1.3 75.5 - - - +
73C LEU* 1.3 60.7 + - - +
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Residues in contact with LEU 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A GLU* 2.9 23.6 - - - +
37B GLN* 4.3 1.9 - - - +
7C VAL* 3.8 20.2 - - + -
8C LYS 2.8 10.1 + - - +
9C MET* 3.7 27.5 - - + +
10C LEU 4.1 0.5 + - - -
32C ILE* 3.9 14.6 - - + -
36C ILE* 3.8 29.2 - - + -
38C VAL* 4.9 1.8 - - + -
43C GLN* 3.9 22.9 - - + -
44C ARG 3.7 1.3 - - - +
45C LEU* 3.8 20.4 - - + -
71C VAL 4.1 0.4 + - - -
72C LEU* 1.3 71.6 - - - +
74C VAL* 1.3 73.5 + - - +
75C VAL* 4.3 12.8 - - + -
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Residues in contact with VAL 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A VAL* 4.8 9.2 - - + +
88A LEU* 4.7 7.2 - - + -
91A MET* 3.6 39.9 - - + +
93A PRO* 5.2 7.9 - - + -
101A GLU* 3.1 27.1 + - - +
37B GLN* 3.5 13.5 - - - +
42C GLN 3.6 0.2 - - - +
44C ARG* 3.1 50.5 + - + +
73C LEU* 1.3 75.7 - - - +
75C VAL* 1.3 64.8 + - - +
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Residues in contact with VAL 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A MET* 4.4 5.1 - - - +
33B ARG* 4.6 1.7 - - - +
36B TRP* 3.2 49.1 - - + +
37B GLN* 2.8 35.5 + - - +
9C MET* 4.0 20.0 - - + -
38C VAL* 4.0 34.3 - - + -
42C GLN* 3.6 14.6 - - + +
73C LEU* 4.3 7.0 - - + -
74C VAL* 1.3 74.2 - - - +
76C ASP* 1.3 60.1 + - - +
77C LYS* 3.4 6.8 + - - +
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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