Contacts of the strand formed by residues 93 - 99 (chain H) 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 ALA 93 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47H ALA 3.3 12.6 - - - +
48H GLY* 4.0 3.4 - - - -
52H ASP 3.9 5.2 - - - +
53H ALA* 3.5 36.6 - - + +
56H LEU* 3.4 11.9 - - + +
91H LEU 3.5 3.6 + - - -
92H GLU* 1.3 79.4 - - - +
94H MET* 1.3 68.5 + - - +
108H GLY 3.0 24.6 + - - -
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Residues in contact with MET 94 (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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46H PHE* 3.4 4.0 - - - +
47H ALA 2.8 35.7 + - - +
56H LEU* 4.0 0.4 - - - +
93H ALA* 1.3 80.3 - - - +
95H LEU* 1.3 66.4 + - - +
105H ILE* 4.9 2.7 - - + -
106H ILE 3.3 7.9 - - - +
107H THR* 3.8 26.5 - - + -
122H ALA 5.4 0.4 - - - +
123H ILE* 3.4 40.0 - - + +
124H GLY* 4.2 10.3 - - - +
22I LEU* 5.0 14.1 - - + -
27I MET* 4.6 13.5 - - + -
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Residues in contact with LEU 95 (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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44H ALA* 5.1 1.1 - - + -
45H GLY 3.3 10.8 - - - +
46H PHE* 3.1 34.1 - - + -
56H LEU* 3.4 30.1 - - + +
57H PHE* 3.6 37.0 - - + +
60H PHE* 4.1 15.3 - - + -
94H MET* 1.3 74.5 - - - +
96H ILE* 1.3 62.3 + - - +
97H VAL* 3.9 14.1 - - + -
105H ILE* 3.1 10.7 - - - +
106H ILE* 2.7 44.0 + - + +
123H ILE* 3.9 0.9 - - - -
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Residues in contact with ILE 96 (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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3H ILE* 3.6 24.5 - - + +
4H VAL* 4.6 0.9 - - - -
5H SER* 4.0 22.2 - - - +
14H VAL* 4.2 11.0 - - + +
43H LEU 3.4 1.4 - - - +
44H ALA* 3.1 3.8 - - - -
45H GLY 2.7 40.2 + - - +
95H LEU* 1.3 77.2 - - - +
97H VAL* 1.3 66.0 + - - +
103H SER* 5.2 1.3 - - - +
104H LEU 3.3 9.9 - - - +
105H ILE* 4.2 6.3 - - + -
121H LEU* 3.8 28.9 - - + +
123H ILE* 3.6 40.8 - - + +
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Residues in contact with VAL 97 (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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43H LEU 2.9 5.6 - - - +
44H ALA* 4.2 12.1 - - + -
60H PHE* 3.2 50.7 - - + -
71H LEU* 3.9 9.6 - - + -
95H LEU* 4.3 14.8 - - + -
96H ILE* 1.3 80.7 - - - +
98H ALA* 1.3 58.1 + - - +
104H LEU* 2.6 58.7 + - + +
106H ILE* 4.1 12.1 - - + -
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Residues in contact with ALA 98 (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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5H SER* 5.2 0.2 - - - +
12H VAL* 3.9 16.6 - - + -
14H VAL* 4.6 9.6 - - + -
42H VAL* 4.5 0.7 - - - -
43H LEU* 2.5 45.0 + - - +
71H LEU* 4.2 7.4 - - - +
96H ILE* 5.3 0.7 - - + -
97H VAL* 1.3 80.1 - - - +
99H ASP* 1.3 57.3 + - - +
102H GLU 3.1 18.8 - - - +
103H SER* 3.4 18.6 - - - +
172H LEU* 4.6 0.4 - - - -
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Residues in contact with ASP 99 (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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7H ARG* 2.9 18.9 + - - -
12H VAL* 3.7 3.0 - - - +
41H LYS 3.3 16.6 - - - +
42H VAL* 3.6 12.6 - - + -
69H GLY 4.5 4.9 - - - +
71H LEU* 3.6 25.5 + - + +
98H ALA* 1.3 74.1 - - - +
100H GLU* 1.3 68.5 + - - +
101H LYS* 3.1 8.4 + - - +
102H GLU* 2.7 29.0 + - - +
172H LEU* 3.4 13.7 - - - -
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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