Contacts of the strand formed by residues 103 - 108 (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 SER 103 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5M SER* 5.2 6.5 - - - -
7M ARG* 3.2 14.3 + - - +
12M VAL* 5.3 0.9 - - - -
71M LEU* 4.5 0.4 - - - +
96M ILE* 6.4 0.9 - - - -
97M VAL 3.2 7.9 - - - -
98M ALA* 3.2 17.5 - - - -
102M GLU* 1.3 79.4 + - - +
104M LEU* 1.3 75.0 + - - +
115M PRO* 3.3 21.5 - - - +
119M GLN* 3.5 25.0 + - - +
121M LEU* 4.5 6.1 - - - -
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Residues in contact with LEU 104 (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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71M LEU* 5.4 3.4 - - + -
72M LEU* 3.8 29.6 - - + -
75M ALA* 4.1 13.5 - - + -
96M ILE* 3.2 7.1 - - - +
97M VAL* 2.4 56.3 + - + +
102M GLU* 4.3 12.6 - - + +
103M SER* 1.3 88.9 - - - +
105M ILE* 1.3 63.0 + - - +
106M ILE* 5.1 0.4 - - + -
112M VAL* 3.4 26.7 - - + -
113M VAL 3.6 16.2 - - - +
114M GLN* 3.6 26.2 - - + +
115M PRO* 4.3 0.7 - - + -
121M LEU* 3.4 11.6 - - - +
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Residues in contact with ILE 105 (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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94M MET* 4.5 11.2 - - + -
95M LEU 2.9 11.9 - - - +
96M ILE* 4.2 2.2 - - + -
104M LEU* 1.3 78.8 - - - +
106M ILE* 1.3 68.9 + - - +
107M THR* 5.2 3.7 - - + +
111M ASP 3.8 0.7 - - - +
112M VAL* 3.5 4.2 - - - -
113M VAL* 2.9 65.2 + - + +
121M LEU* 3.9 20.0 - - + -
122M ALA 4.8 3.1 - - - +
123M ILE* 3.3 32.5 - - + -
27R MET* 4.4 21.8 - - + -
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Residues in contact with ILE 106 (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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56M LEU* 4.4 6.5 - - + +
60M PHE* 3.5 40.8 - - + -
75M ALA* 4.0 12.8 - - + +
78M LEU* 4.8 17.7 - - + -
79M ALA 5.5 1.8 - - - +
82M TRP* 5.1 3.8 - - + -
94M MET* 3.4 2.0 - - - -
95M LEU* 2.7 49.9 + - + +
97M VAL* 4.0 17.5 - - + -
105M ILE* 1.3 79.5 - - - +
107M THR* 1.3 72.7 + - - +
108M GLY 4.1 0.2 + - - -
111M ASP 3.5 15.5 - - - +
112M VAL* 4.4 16.4 - - + -
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Residues in contact with THR 107 (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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56M LEU* 3.9 2.5 - - - -
82M TRP* 3.9 6.8 - - - -
93M ALA 3.9 4.0 - - - -
94M MET* 3.9 26.9 - - - -
105M ILE* 5.2 7.4 - - + +
106M ILE* 1.3 78.5 - - - +
108M GLY* 1.3 59.0 + - - +
109M ILE* 3.3 23.2 + - + +
110M GLY* 2.9 23.4 + - - -
111M ASP* 2.2 46.6 + - - +
113M VAL* 5.9 2.5 - - + -
22R LEU* 6.6 0.2 - - + -
27R MET* 5.8 7.9 - - + -
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Residues in contact with GLY 108 (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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56M LEU* 3.3 21.2 - - - +
82M TRP* 3.3 20.7 + - - -
90M LYS* 3.7 1.6 - - - -
91M LEU* 2.9 42.8 + - - -
93M ALA 3.0 13.5 + - - -
107M THR* 1.3 71.5 - - - +
109M ILE* 1.3 58.1 + - - +
110M GLY 3.3 0.4 - - - -
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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