Contacts of the strand formed by residues 46 - 51 (chain B) in PDB entry 3DGG
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 46 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B VAL* 3.3 4.5 - - - -
38B LYS* 2.8 73.2 + - + +
40B LYS* 4.1 14.6 + - - +
43B GLN* 5.5 0.9 - - - +
44B GLY 4.6 6.1 - - - +
45B LEU* 1.3 75.8 - - - +
47B TRP* 1.3 64.6 + - - +
48B ILE* 3.6 0.5 + - - +
61B ASN* 5.4 2.7 - - - +
63B LYS* 2.8 38.1 + - + +
64B PHE* 4.5 8.7 - - + -
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Residues in contact with TRP 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU* 4.5 19.1 - - + -
99A LEU* 3.3 58.2 - - + +
100A THR* 6.0 0.2 - - - -
101A PHE* 5.0 6.2 - - + -
35B HIS* 3.1 24.2 + + - -
36B TRP 3.6 15.5 - - - -
37B VAL* 4.5 3.6 - - - +
45B LEU 4.1 2.0 + - - -
46B GLU* 1.3 71.5 - - - +
48B ILE* 1.3 59.6 + - - +
49B GLY* 3.4 30.1 + - - -
50B TYR* 3.9 14.4 - + - -
59B ASN* 4.1 11.7 - - - -
60B TYR 4.2 2.2 - - - -
61B ASN* 2.8 63.4 + - + +
64B PHE* 3.6 3.6 - - - -
106B TRP* 3.8 9.9 - + - -
31C THR 3.8 20.2 - - - -
32C SER* 4.8 1.8 - - - -
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Residues in contact with ILE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B TRP* 3.0 16.2 + - + +
37B VAL 3.7 24.9 - - - +
38B LYS* 3.7 12.8 - - + +
47B TRP* 1.3 76.3 - - - +
49B GLY* 1.3 60.3 + - - +
60B TYR* 3.4 9.4 - - + +
61B ASN* 3.0 23.6 + - - +
64B PHE* 3.8 29.7 - - + +
68B ALA* 3.8 28.3 - - + -
70B LEU* 4.8 5.2 - - + -
81B MET* 3.7 27.6 - - + -
83B LEU* 5.5 1.1 - - + -
94B TYR* 3.7 17.7 - - + -
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Residues in contact with GLY 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B HIS* 3.5 0.3 - - - -
36B TRP* 3.0 24.9 + - - -
47B TRP* 3.4 22.8 + - - -
48B ILE* 1.3 81.2 - - - +
50B TYR* 1.3 60.7 + - - -
59B ASN 3.1 14.6 - - - -
60B TYR* 4.1 1.6 - - - -
70B LEU* 3.5 12.7 - - - +
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Residues in contact with TYR 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B VAL* 3.7 11.9 - - + -
34B MET 3.2 12.3 - - - +
35B HIS* 3.5 20.6 - - + +
47B TRP* 4.0 7.6 - + - -
49B GLY* 1.3 74.5 - - - -
51B ILE* 1.3 70.1 + - - +
52B ASN* 3.8 9.0 - - + -
57B ASP* 3.1 36.8 + - - -
58B THR* 3.3 22.9 + - - +
59B ASN* 3.1 39.0 + - + +
70B LEU* 3.5 8.6 - - - +
30C SER* 2.6 31.8 + - - -
31C THR 4.0 2.2 - - - -
32C SER 4.0 4.3 - - - -
33C GLY* 3.5 30.7 + - - -
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Residues in contact with ILE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B PHE* 6.4 0.2 - - + -
33B VAL* 3.7 0.9 - - - -
34B MET* 2.9 47.2 + - + +
36B TRP* 4.9 4.7 - - - +
50B TYR* 1.3 78.8 - - - +
52B ASN* 1.3 63.3 + - - +
53B PRO* 3.3 5.2 - - + +
56B ASP* 3.9 18.6 - - + +
57B ASP 3.5 6.3 - - - +
58B THR* 3.1 28.5 - - + -
70B LEU* 3.7 23.6 - - + +
71B THR* 4.0 14.6 - - - +
72B SER* 4.1 21.5 - - - +
79B ALA* 4.4 15.5 - - + -
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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