Contacts of the strand formed by residues 42 - 48 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36I ARG* 3.4 6.9 - - - +
37I LEU* 3.0 63.8 + - + +
38I TYR* 3.9 7.2 - - + +
40I GLY 3.7 0.8 - - - -
41I LYS* 1.3 87.1 - - + +
43I LEU* 1.3 69.0 + - - +
60I PHE* 5.5 0.7 - - + -
64I LEU* 3.6 23.8 - - + -
69I GLY 5.1 4.7 - - - +
71I LEU* 3.9 19.5 - - + -
98I ALA 3.6 3.8 - - - +
99I ASP* 3.5 20.4 - - + +
172I LEU* 4.7 0.4 - - - -
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Residues in contact with LEU 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I VAL* 4.0 16.2 - - + +
14I VAL* 3.5 30.5 - - + +
34I VAL* 5.1 0.9 - - + -
35I ARG 3.8 2.2 - - - +
36I ARG* 3.6 35.2 - - + +
42I VAL* 1.3 81.3 - - - +
44I ALA* 1.3 62.7 + - - +
96I ILE 4.0 1.6 - - - -
97I VAL* 2.9 6.9 - - - +
98I ALA 2.6 41.2 + - - +
170I GLU* 3.0 36.3 - - + +
171I GLU 4.0 4.9 - - - -
172I LEU* 3.8 15.0 - - + -
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Residues in contact with ALA 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I LYS 3.9 0.5 - - - +
34I VAL* 3.2 5.8 - - - +
35I ARG 2.9 37.5 + - - +
37I LEU* 3.8 15.5 - - + -
43I LEU* 1.3 77.5 - - - +
45I GLY* 1.3 60.0 - - - +
46I PHE* 4.1 0.7 + - - -
57I PHE* 3.5 33.1 - - + -
60I PHE* 5.4 0.2 - - + -
95I LEU* 5.1 2.2 - - + -
96I ILE 3.1 5.8 - - - +
97I VAL* 4.1 10.3 - - + -
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Residues in contact with GLY 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I ILE* 3.5 10.3 - - - -
14I VAL* 4.0 7.1 - - - +
33I LYS 3.3 9.0 - - - -
34I VAL* 3.6 15.0 - - - -
44I ALA* 1.3 74.1 - - - +
46I PHE* 1.3 60.0 + - - -
95I LEU* 3.2 4.5 - - - -
96I ILE* 2.6 42.3 + - - +
123I ILE* 3.6 4.2 - - - +
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Residues in contact with PHE 46 (chain I).
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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444B LEU* 5.2 6.3 - - + -
1I THR* 4.6 1.0 - - - +
3I ILE* 2.9 13.4 - - - +
32I ARG 3.8 17.9 - - - -
33I LYS* 3.0 31.9 + - + +
35I ARG* 4.1 18.6 - - + -
44I ALA 4.7 0.7 - - - -
45I GLY* 1.3 72.2 - - - -
47I ALA* 1.3 62.5 + - - +
50I THR* 6.3 0.2 - - - -
53I ALA* 3.6 25.8 - - + -
54I PHE* 3.3 35.9 - + - -
57I PHE* 3.6 37.9 - + + -
94I MET 3.4 4.5 - - - +
95I LEU* 3.1 18.2 - - + -
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Residues in contact with ALA 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1I THR* 4.2 14.1 - - + -
3I ILE* 3.9 6.3 - - + -
46I PHE* 1.3 77.1 - - - +
48I GLY* 1.3 58.5 + - - +
53I ALA* 4.9 0.9 - - - -
93I ALA* 3.3 3.8 - - - -
94I MET* 2.8 38.8 + - + +
123I ILE* 3.7 25.5 - - + +
124I GLY* 4.0 20.2 - - - +
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Residues in contact with GLY 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1I THR* 4.8 9.7 + - - -
47I ALA* 1.3 75.2 - - - +
49I GLY* 1.3 65.0 - - - -
50I THR* 3.5 3.1 + - - +
53I ALA* 4.7 2.8 - - - +
92I GLU 3.5 12.6 - - - -
93I ALA* 4.0 2.2 - - - -
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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