Contacts of the strand formed by residues 45 - 50 (chain C) in PDB entry 3DH1
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 GLY 45 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ALA* 3.5 23.0 - - - +
32C MET* 4.0 13.5 - - - -
33C ALA* 3.9 10.2 - - - +
44C VAL* 1.3 75.9 - - - +
46C CYS* 1.3 64.9 + - - +
58C GLY 3.6 5.4 - - - -
59C ARG* 4.5 0.4 - - - -
72C ALA* 4.5 0.4 - - - -
102C VAL* 3.6 0.9 - - - +
103C THR* 3.2 26.2 + - - -
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Residues in contact with CYS 46 (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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29C ALA* 4.2 3.1 - - - +
32C MET* 4.1 5.3 - - - +
45C GLY* 1.3 74.6 - - - -
47C LEU* 1.3 63.4 + - - +
57C LYS* 3.4 3.5 - - - -
58C GLY 3.0 32.6 + - - -
72C ALA* 3.5 34.3 - - + -
73C GLU* 3.9 4.9 - - - -
76C ALA* 3.8 11.2 - - - -
100C LEU* 3.7 19.3 - - + -
101C TYR 3.1 17.0 - - - +
102C VAL* 3.1 17.9 - - + -
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Residues in contact with LEU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C TRP* 3.2 35.4 - - + +
28C GLU* 3.7 16.8 - - + +
29C ALA* 3.6 18.6 - - + +
32C MET* 4.7 4.0 - - - -
46C CYS* 1.3 76.5 - - - +
48C MET* 1.3 63.2 + - - +
49C VAL* 4.9 6.5 - - + -
54C VAL* 3.7 19.7 - - + -
56C GLY 3.4 3.6 - - - -
57C LYS* 3.4 39.5 - - + +
100C LEU* 3.4 6.6 - - - +
101C TYR* 3.0 40.5 + - + -
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Residues in contact with MET 48 (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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47C LEU* 1.3 73.7 - - - +
49C VAL* 1.3 61.6 + - - +
54C VAL* 3.7 2.1 - - - -
55C VAL* 2.8 30.3 + - - +
56C GLY 2.8 13.7 + - - +
73C GLU 5.1 0.2 - - - +
76C ALA* 3.7 22.4 - - + -
77C ILE* 4.1 11.4 - - + -
80C VAL* 3.6 24.0 - - + -
95C PHE* 3.8 26.0 - - + -
98C THR* 3.9 14.6 - - + -
99C VAL 3.5 3.6 - - - -
100C LEU* 3.3 32.1 - - + -
114C LEU* 5.4 1.8 - - + -
119C ILE* 3.8 28.5 - - + -
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Residues in contact with VAL 49 (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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17C GLN* 4.0 21.1 - - + +
25C TRP* 3.4 48.7 - - + +
47C LEU* 4.9 2.2 - - + -
48C MET* 1.3 79.9 - - - +
50C TYR* 1.3 63.4 + - - +
52C ASN* 4.2 2.5 - - - +
53C GLU 3.2 23.6 - - - +
54C VAL* 4.4 9.0 - - + -
97C HIS 4.2 0.9 - - - +
98C THR* 3.4 5.8 - - - +
99C VAL* 3.0 31.5 + - - +
101C TYR* 3.8 15.5 - - + +
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Residues in contact with TYR 50 (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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14C LEU* 4.2 20.7 - - + +
48C MET 4.2 0.2 + - - -
49C VAL* 1.3 75.3 - - - +
51C ASN* 1.3 87.6 + - + +
52C ASN 3.2 0.7 - - - -
53C GLU* 2.8 26.0 + - - +
55C VAL* 4.0 15.5 - - + +
83C TRP* 4.3 28.7 - + - -
89C LYS* 3.8 24.7 + - - +
93C GLU* 4.1 14.9 + - - +
94C VAL* 3.5 40.6 - - + -
97C HIS* 3.5 30.1 - - + -
98C THR* 3.8 9.0 - - - +
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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