Contacts of the strand formed by residues 46 - 51 (chain H) in PDB entry 3GBN
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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H VAL* 3.9 3.6 - - - -
38H ARG* 2.8 67.4 + - + +
40H ALA* 5.6 5.0 + - - +
44H GLY 4.5 5.8 - - - +
45H PRO* 1.3 78.3 - - - +
47H TRP* 1.3 67.2 + - - +
48H MET* 3.4 4.2 + - - +
62H LYS* 2.5 40.8 + - - +
63H PHE* 4.1 8.4 - - + -
98L PHE* 4.3 1.3 - - - -
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Residues in contact with TRP 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H SER* 2.8 34.5 + - - -
36H TRP 3.9 3.8 - - - -
37H VAL* 3.9 16.2 - - + -
46H GLU* 1.3 73.7 - - - +
48H MET* 1.3 57.1 + - - +
49H GLY* 3.4 19.0 + - - -
50H GLY 3.7 1.1 - - - -
58H LYS* 3.6 29.4 - - + -
59H TYR 3.9 1.6 - - - -
60H ALA* 3.2 39.5 - - + +
63H PHE* 4.0 4.3 - - - -
95H HIS* 4.7 0.4 + - - -
100H MET* 3.4 27.3 - - + +
91L TRP* 4.8 2.0 - + - -
95L TYR* 3.4 34.4 - - - -
96L VAL* 3.6 56.3 + - + +
98L PHE* 3.9 9.6 - - + -
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Residues in contact with MET 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H TRP* 2.8 30.5 + - + +
38H ARG* 4.0 9.9 - - + +
46H GLU 3.9 8.7 - - - +
47H TRP* 1.3 75.9 - - - +
49H GLY* 1.3 54.4 + - - +
59H TYR* 3.6 8.9 - - - +
60H ALA* 3.0 23.8 + - - +
63H PHE* 3.7 49.2 - - + +
67H VAL* 4.3 9.1 - - + +
69H ILE* 5.0 0.9 - - + -
80H MET* 4.0 19.5 - - - -
82H LEU* 4.1 15.5 - - + -
90H TYR* 3.6 38.6 - - + -
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Residues in contact with GLY 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H SER* 3.1 3.8 - - - -
36H TRP 2.9 25.7 + - - -
47H TRP* 3.4 18.8 - - - -
48H MET* 1.3 80.3 - - - +
50H GLY* 1.3 58.9 + - - -
58H LYS 3.0 15.7 - - - -
59H TYR* 4.1 1.1 - - - -
69H ILE* 3.2 14.7 - - - +
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Residues in contact with GLY 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H ILE 3.2 13.2 - - - -
35H SER* 3.6 9.9 - - - -
47H TRP* 3.7 3.2 - - - -
49H GLY* 1.3 75.0 - - - -
51H ILE* 1.3 60.6 + - - -
52H ILE* 5.3 0.3 - - - +
56H THR 4.0 0.2 - - - +
57H THR* 3.3 6.1 - - - -
58H LYS 3.0 29.5 + - - +
69H ILE* 3.5 9.3 - - - +
100H VAL* 3.9 12.2 - - - +
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Residues in contact with ILE 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H ARG* 4.6 5.3 + - - +
33H ALA* 3.2 18.4 - - - +
34H ILE* 3.0 20.6 + - + +
50H GLY* 1.3 74.6 - - - +
52H ILE* 1.3 74.3 + - - +
55H GLY* 3.8 20.9 - - - +
56H THR 3.4 11.7 - - - +
57H THR* 3.8 10.8 - - + -
69H ILE* 3.7 22.9 - - + +
70H THR* 4.1 5.6 - - - -
71H ALA* 4.0 31.6 - - + +
78H VAL* 4.3 21.8 - - + -
100H VAL* 4.2 1.4 - - - +
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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