Contacts of the strand formed by residues 104 - 109 (chain B) in PDB entry 1M54
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 GLU 104 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ILE* 4.3 3.8 - - - +
91B ARG* 3.9 20.6 + - + +
103B CYS* 1.3 75.4 - - - +
105B LEU* 1.3 57.6 + - - +
106B LEU* 2.9 38.1 + - + +
367B GLY 5.9 0.9 - - - -
368B GLN 3.0 13.9 + - - +
369B ARG* 2.6 40.6 + - - +
370B CYS 3.5 17.2 + - - -
134C GLY 4.5 1.4 - - - +
137C LYS* 3.3 40.8 + - + +
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Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ARG* 3.5 3.3 - - - +
92B ILE* 2.6 63.4 + - + +
95B ILE 5.0 0.9 - - - -
96B GLY* 3.7 21.3 - - - +
101B LEU* 3.2 34.5 - - + -
103B CYS 3.7 4.6 + - - +
104B GLU* 1.3 68.5 - - - +
106B LEU* 1.3 61.1 + - - +
354B VAL* 4.7 12.8 - - + -
357B ALA* 4.1 24.5 - - + -
358B VAL* 5.2 3.1 - - + -
370B CYS* 3.8 23.3 - - + +
372B VAL* 4.5 5.8 - - + -
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ILE* 3.2 48.0 - - + -
89B MET* 3.8 17.0 - - + -
90B VAL 3.1 11.4 - - - -
91B ARG* 4.5 2.7 - - - +
92B ILE* 4.7 0.3 - - - +
104B GLU* 2.9 35.8 + - + +
105B LEU* 1.3 77.5 - - - +
107B ALA* 1.3 63.0 + - - +
244B CYS* 4.4 9.0 - - - -
369B ARG* 3.3 39.3 - - + -
370B CYS 3.4 8.2 + - - +
371B VAL* 4.5 6.5 - - + -
372B VAL* 3.5 23.2 + - - +
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B PRO 3.6 0.5 - - - +
89B MET* 3.9 2.0 - - - -
90B VAL* 2.5 36.9 + - + +
92B ILE* 4.3 17.7 - - + -
106B LEU* 1.3 79.1 - - - +
108B LYS* 1.3 59.8 + - - +
109B CYS* 2.9 17.1 + - - -
344B LEU* 5.0 1.1 - - + -
372B VAL* 3.9 9.2 - - + -
374B LEU* 3.8 27.1 - - + -
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Residues in contact with LYS 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B THR* 3.1 27.5 + - - -
88B PRO 3.6 3.8 - - - +
89B MET* 3.5 16.4 - - + -
107B ALA* 1.3 66.8 - - - +
109B CYS* 1.3 60.1 + - - +
110B GLU* 3.1 21.3 + - - +
121B ARG* 4.2 0.2 - - - +
236B THR* 4.5 7.2 - - - -
239B GLU* 2.8 30.7 + - - +
240B ILE* 3.3 38.6 - - + -
243B GLN* 3.5 19.1 + - - +
371B VAL* 3.7 7.9 - - + -
372B VAL 2.8 15.4 + - - +
373B ILE* 3.8 10.5 - - + -
374B LEU* 3.0 23.8 + - - +
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Residues in contact with CYS 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B THR* 3.4 19.7 - - - +
88B PRO* 3.1 10.1 + - + +
90B VAL* 3.8 26.0 - - - -
107B ALA* 2.9 23.8 + - - -
108B LYS* 1.3 68.7 - - - +
110B GLU* 1.3 64.8 + - - +
111B PHE* 3.2 27.5 + - + -
112B PHE* 3.7 19.3 + - + -
344B LEU* 4.0 18.8 - - - -
374B LEU* 4.1 9.4 - - - -
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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