Contacts of the strand formed by residues 42 - 48 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36M ARG* 3.7 4.2 - - - +
37M LEU* 2.9 60.3 + - + +
38M TYR* 4.3 2.7 - - + -
40M GLY 5.0 1.0 - - - -
41M LYS* 1.3 86.1 + - + +
43M LEU* 1.3 68.8 + - - +
44M ALA* 5.9 0.9 - - + -
60M PHE* 5.3 1.8 - - + -
64M LEU* 3.4 24.2 - - + -
69M GLY* 5.0 6.3 - - - +
71M LEU* 4.0 23.1 - - + -
97M VAL* 5.7 0.7 - - + -
98M ALA 3.7 5.4 - - - +
99M ASP* 3.5 22.2 - - + +
172M LEU* 4.6 0.4 - - - -
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Residues in contact with LEU 43 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M VAL* 3.7 24.5 - - + +
14M VAL* 4.3 19.1 - - + -
34M VAL* 5.1 0.7 - - + -
35M ARG 4.0 2.5 - - - +
36M ARG* 3.6 30.1 - - + +
42M VAL* 1.3 74.0 - - - +
44M ALA* 1.3 62.0 + - - +
96M ILE 3.6 1.1 - - - +
97M VAL* 3.1 8.5 - - - +
98M ALA 2.7 35.8 + - - +
170M GLU* 3.4 48.0 - - + +
171M GLU* 4.0 0.9 - - - -
172M LEU* 3.6 28.5 - - + -
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Residues in contact with ALA 44 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14M VAL* 4.7 0.2 - - - -
33M LYS 3.9 0.5 - - - +
34M VAL* 3.1 7.2 - - - +
35M ARG* 2.8 41.3 + - - +
37M LEU* 4.8 9.6 - - + -
42M VAL* 4.1 0.9 + - + -
43M LEU* 1.3 77.1 - - - +
45M GLY* 1.3 59.3 + - - +
46M PHE* 4.2 2.4 + - - -
57M PHE* 3.5 33.7 - - + -
95M LEU* 5.1 2.0 - - + -
96M ILE 3.3 4.0 - - - -
97M VAL* 4.1 15.7 - - + -
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Residues in contact with GLY 45 (chain M).
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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3M ILE* 4.0 20.4 - - - -
14M VAL* 4.3 2.3 - - - +
33M LYS 3.3 9.4 - - - -
34M VAL* 4.1 6.1 - - - -
44M ALA* 1.3 74.5 - - - +
46M PHE* 1.3 61.4 + - - -
95M LEU* 3.4 5.4 - - - -
96M ILE* 2.8 41.6 + - - +
123M ILE* 3.7 5.0 - - - +
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Residues in contact with PHE 46 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1M THR* 3.9 3.8 - - - +
3M ILE* 3.5 15.7 - - - +
32M ARG 3.1 22.9 - - - -
33M LYS* 3.0 36.4 + - + +
35M ARG* 4.1 16.6 - - + -
44M ALA 4.7 3.1 - - - -
45M GLY* 1.3 75.5 - - - -
47M ALA* 1.3 65.6 + - - +
48M GLY 5.6 0.2 - - - -
50M THR* 6.3 0.2 - - - -
53M ALA* 3.7 30.3 - - + +
54M PHE* 3.5 33.4 - + - -
57M PHE* 4.8 14.1 - + + -
93M ALA* 6.0 0.2 - - + -
94M MET 3.5 4.5 - - - -
95M LEU* 3.4 20.9 - - + -
444T LEU* 5.2 8.7 - - + -
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Residues in contact with ALA 47 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1M THR* 3.7 20.9 - - + -
3M ILE* 3.9 4.7 - - + -
46M PHE* 1.3 79.6 - - - +
48M GLY* 1.3 58.8 + - - +
53M ALA* 5.2 0.2 - - - -
93M ALA* 3.2 4.8 - - - +
94M MET* 2.8 37.0 + - + +
123M ILE* 3.6 20.6 - - + -
124M GLY* 3.9 20.9 - - - +
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Residues in contact with GLY 48 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1M THR* 4.7 10.3 + - - -
46M PHE* 5.6 0.2 - - - -
47M ALA* 1.3 75.6 - - - +
49M GLY* 1.3 64.5 + - - -
50M THR* 3.4 3.6 + - - +
53M ALA* 4.6 5.2 - - - +
92M GLU 3.5 10.5 - - - -
93M ALA* 3.6 4.3 - - - -
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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