Contacts of the strand formed by residues 42 - 48 (chain L) in PDB entry 1G3I
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 VAL 42 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36L ARG* 3.4 6.6 - - - +
37L LEU* 3.0 67.3 + - + +
38L TYR* 4.0 6.1 - - + -
40L GLY 3.7 0.6 - - - -
41L LYS* 1.3 88.8 - - + +
43L LEU* 1.3 69.3 + - - +
60L PHE* 5.4 0.7 - - + -
64L LEU* 3.5 24.2 - - + -
69L GLY 5.1 4.7 - - - +
71L LEU* 4.0 17.5 - - + -
98L ALA 3.7 3.8 - - - +
99L ASP* 3.6 18.6 - - + +
172L LEU* 4.8 0.4 - - - -
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Residues in contact with LEU 43 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L VAL* 3.9 19.1 - - + +
14L VAL* 3.8 25.6 - - + -
34L VAL* 5.2 0.9 - - + -
35L ARG 3.9 2.0 - - - +
36L ARG* 3.6 35.7 - - + +
42L VAL* 1.3 81.6 - - - +
44L ALA* 1.3 63.1 + - - +
60L PHE* 5.6 0.2 - - - -
96L ILE 4.2 1.3 - - - -
97L VAL* 3.1 6.2 - - - +
98L ALA 2.6 41.4 + - - +
170L GLU* 3.0 37.9 - - + +
171L GLU 3.9 5.2 - - - -
172L LEU* 3.8 14.6 - - + -
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Residues in contact with ALA 44 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14L VAL* 5.0 0.2 - - - +
33L LYS 4.1 0.5 - - - +
34L VAL* 3.3 5.4 - - - +
35L ARG 2.9 36.9 + - - +
37L LEU* 3.7 17.5 - - + -
43L LEU* 1.3 77.3 - - - +
45L GLY* 1.3 61.1 + - - +
46L PHE* 4.2 0.9 + - - -
57L PHE* 3.6 32.9 - - + -
60L PHE* 5.3 0.4 - - + -
95L LEU* 5.3 1.6 - - + -
96L ILE 3.2 5.4 - - - -
97L VAL* 4.2 11.2 - - + -
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Residues in contact with GLY 45 (chain L).
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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3L ILE* 3.5 10.1 - - - -
14L VAL* 4.1 6.7 - - - +
33L LYS 3.3 9.4 - - - -
34L VAL* 3.7 15.0 - - - -
44L ALA* 1.3 76.1 - - - +
46L PHE* 1.3 60.5 + - - -
95L LEU* 3.1 6.1 - - - +
96L ILE 2.7 34.6 + - - -
123L ILE* 3.8 2.6 - - - +
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Residues in contact with PHE 46 (chain L).
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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444E LEU* 5.3 6.1 - - + -
1L THR* 4.8 1.0 - - - +
3L ILE* 3.0 13.8 - - - +
32L ARG 3.9 17.0 - - - -
33L LYS* 3.0 31.6 + - + +
35L ARG* 4.3 16.2 - - + -
44L ALA 4.7 1.3 - - - -
45L GLY* 1.3 73.4 - - - -
47L ALA* 1.3 61.2 + - - +
53L ALA* 3.6 26.7 - - + -
54L PHE* 3.5 37.2 - + - -
57L PHE* 3.8 35.4 - + + -
94L MET 3.4 4.0 - - - +
95L LEU* 3.0 19.1 - - + -
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Residues in contact with ALA 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1L THR* 4.3 15.9 - - + -
3L ILE* 4.1 6.3 - - + -
46L PHE* 1.3 77.3 - - - +
48L GLY* 1.3 58.9 + - - +
53L ALA* 4.9 0.9 - - - -
93L ALA* 3.3 3.6 - - - -
94L MET* 2.8 38.9 + - + +
123L ILE* 3.8 23.8 - - + +
124L GLY* 4.0 21.1 - - - +
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Residues in contact with GLY 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1L THR* 5.1 8.0 + - - -
47L ALA* 1.3 75.8 - - - +
49L GLY* 1.3 65.4 + - - -
50L THR* 3.4 4.2 + - - +
53L ALA* 4.6 3.2 - - - +
92L GLU 3.5 12.1 - - - -
93L ALA* 3.8 3.3 - - - +
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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