Contacts of the strand formed by residues 37 - 42 (chain C) 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 MET 37 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C LEU* 3.6 32.8 - - + -
23C CYS* 3.7 19.3 - - + -
25C ALA* 5.5 0.7 - - + -
29C VAL* 3.6 26.7 - - + -
35C SER 2.7 11.7 + - - +
36C TYR* 1.3 73.1 - - - +
38C HIS* 1.3 61.3 + - - +
39C TRP* 5.3 4.0 - - - +
54C LEU* 3.2 5.7 + - - +
55C ALA* 2.7 33.2 + - - +
75C PHE* 3.7 35.4 - - + -
92C CYS* 4.1 7.6 - - + -
93C GLN 3.3 12.8 - - - +
94C HIS* 3.8 24.7 - - - -
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Residues in contact with HIS 38 (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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36C TYR 4.5 2.2 - - - -
37C MET* 1.3 77.4 - - - +
39C TRP* 1.3 65.4 + - - +
40C TYR* 3.7 22.0 + - + -
50C LEU* 4.0 5.4 - - + -
52C ILE 3.4 7.6 - - - +
53C TYR* 3.6 12.1 - - + +
54C LEU* 3.2 32.0 + - - +
92C CYS* 3.3 6.6 - - - +
93C GLN* 2.9 49.9 + - - +
95C SER* 2.9 32.6 - - - -
103D GLY 3.1 17.0 + - - -
104D SER 3.3 15.5 + - - -
105D ARG* 3.8 4.6 - - + +
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Residues in contact with TRP 39 (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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6C GLN* 3.8 7.0 - - - -
21C ILE* 3.8 36.8 - - + -
22C SER 4.2 1.1 - - - -
23C CYS* 3.7 31.2 - - + -
37C MET* 5.2 5.9 - - + +
38C HIS* 1.3 78.5 + - - +
40C TYR* 1.3 62.8 + - - +
50C LEU* 3.5 6.1 - - - +
51C LEU* 2.9 27.6 + - + -
52C ILE* 2.9 41.4 + - + +
55C ALA* 4.6 8.6 + - - +
68C GLY* 5.2 0.2 - - - -
69C SER 5.4 0.4 + - - -
75C PHE* 4.1 13.8 - - + +
76C THR 4.0 14.8 + - - -
77C LEU* 3.7 46.4 - - + -
90C TYR* 4.9 1.3 - - + -
91C TYR 3.4 10.5 - - - -
92C CYS* 3.7 30.7 - - + -
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Residues in contact with TYR 40 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C HIS* 3.7 10.3 + - + +
39C TRP* 1.3 76.0 - - - +
41C GLN* 1.3 60.7 + - - +
48C PRO* 4.1 16.2 - - + -
49C LYS 3.1 7.0 - - - +
50C LEU* 3.4 36.2 - - + +
51C LEU* 4.3 4.0 - - - +
89C THR 4.0 0.2 - - - +
90C TYR* 3.3 8.8 - - - +
91C TYR* 2.8 47.6 + - + +
93C GLN* 3.0 45.6 + - + -
101C PHE* 4.0 13.7 - + + -
45D LEU* 5.7 0.2 - - + -
106D TRP* 3.3 42.1 + - + +
109D TRP* 3.8 22.7 - + - -
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Residues in contact with GLN 41 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40C TYR* 1.3 72.5 - - - +
42C GLN* 1.3 63.4 + - - +
43C LYS* 4.1 18.7 - - - +
47C PRO 4.2 0.7 - - - +
48C PRO* 3.4 1.2 - - - +
49C LYS* 2.6 64.0 + - - +
51C LEU* 3.4 26.7 - - + +
66C PHE* 3.8 12.5 - - - -
85C GLU 4.2 9.5 - - - +
86C ASP* 4.4 0.5 - - - +
88C ALA* 3.6 17.7 - - + -
89C THR 3.5 3.6 - - - -
90C TYR* 3.0 32.3 + - + -
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Residues in contact with GLN 42 (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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41C GLN* 1.3 75.8 - - - +
43C LYS* 1.3 66.6 + - - +
44C PRO* 4.7 0.7 - - - +
46C GLN 3.2 26.8 - - - +
47C PRO 4.1 1.3 - - - -
48C PRO* 3.7 23.7 - - + +
88C ALA* 3.5 2.7 - - - +
89C THR* 2.8 42.7 + - - +
91C TYR* 3.3 26.5 + - + -
39D GLN* 2.7 45.8 + - - -
45D LEU* 4.6 0.2 - - - +
95D TYR* 3.4 4.2 + - - -
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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